Pirin polypeptide and immune modulation

ABSTRACT

The present invention relates to polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in the treatment and/or prevention of a disorder in a subject; wherein said disorder is an inflammatory disorder and/or an autoimmune disorder; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Feb. 12, 2021, is named 56708_707_303_SL.txt and is 16,384 bytes in size.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No. 16/560,381, filed Sep. 4, 2019, which is a division of U.S. application Ser. No. 15/631,952, filed Jun. 23, 2017, now U.S. Pat. No. 10,456,444, issued Oct. 29, 2019, which is a continuation of International Application No. PCT/GB2015/054113, filed Dec. 22, 2015, which claims the benefit of Great Britain Application No. 1423083.3, filed Dec. 23, 2014, which are hereby incorporated by reference in their entirety.

FIELD OF INVENTION

The present invention relates to the polypeptide HP or a polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence for various therapeutic and nutritional uses.

BACKGROUND

Bacteroides thetaiotaomicron has potent anti-inflammatory effects in vitro and in vivo (Kelly et al. Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA. Nat Immunol. 2004 January; 5(1):104-12). It modulates molecular signalling pathways of NF-κβ (Kelly et al, Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA. Nat Immunol. 2004 January; 5(1):104-12). In particular, it stops binding of the active component (RelA) of NF-κβ to key genes in the nucleus, thereby preventing the activation of pro-inflammatory pathways (Kelly et al, Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA. Nat Immunol. 2004 January; 5(1):104-12).

The full genome of B. thetaiotaomicron was sequenced and annotated by the Gordon Group (Washington University School of Medicine, USA) in 2003 [Xu et al, A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003 Mar. 28; 299(5615):2074-6].

STATEMENTS OF INVENTION

Surprisingly, the present inventors found that HP (a hypothetical protein; gene ID 1075517; gene symbol BT_0187; accession number AAO75294) identified from the genome of Bacteroides thetaiotaomicron (VP15482), a pirin-related protein; deposited as AAO75294.1, which reduces inflammation in cells.

The present invention provides polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in the treatment and/or prevention of a disorder in a subject; wherein said disorder is an inflammatory disorder and/or an autoimmune disorder; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in modulating the inflammation of a cell, a tissue or an organ in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in improving intestine barrier integrity in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in modifying the bacterial composition in a tissue or organ to provide a more beneficial microbiota. For example, the invention may be of use in reducing the level of one or more types of lactose fermenting bacteria (such as E. coli) in a tissue or an organ in a subject and/or reducing the level of one or more types of non-lactose fermenting bacteria in a tissue or an organ in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in maintaining the length of the large intestine and/or small intestine of a subject, (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in reducing disruption to the intestine (such as the large intestine) of a subject, (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in regulating the expression of one or more pro-inflammatory genes and/or one or more barrier integrity genes in a cell or cells of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in regulating the expression in a cell or cells of a subject of one or more genes selected from the group consisting of regenerating islet-derived 3 beta gene (Reg3b), resistin-like gamma resistin like beta gene (RetnIg|Retnlb), sucrase-isomaltase (alpha-glucosidase) gene (Si), defensin alpha 24 gene (Defa24), hydroxysteroid 11-beta dehydrogenase 2 gene (Hsd11b2), hydroxysteroid (17-beta) dehydrogenase 2 gene (Hsd17b2), resistin-Like Molecule-beta (RELMb), and nuclear receptor 1D1 thyroid hormone receptor alpha gene (Nr1d1|Thra); (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides polypeptide HP or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in reducing the activation of pro-inflammatory pathways in a cell or cells of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in reducing the activity and/or expression of NF-κβ in a cell or cells (such as epithelial cells, epidermal cells, neuronal cells, and/or pancreatic cells) of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for use in improving alimentary canal health in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, a pharmaceutical composition comprising polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, and a pharmaceutically acceptable excipient, carrier or diluent; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides a nutritional supplement comprising polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, and a nutritional acceptable excipient, carrier or diluent; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides a feedstuff, food product, dietary supplement, or food additive comprising polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides in a further aspect a process for producing a pharmaceutical composition according to the present invention, said process comprising admixing polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence with a pharmaceutically acceptable excipient, carrier or diluent; optionally said polypeptide or polynucleotide sequence or host cell is encapsulated in said process; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides a process for producing a nutritional supplement according to the present invention, said process comprising admixing polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence with a nutritionally acceptable excipient, carrier or diluent; optionally said polypeptide or polynucleotide is encapsulated in said process; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides a process for producing a feedstuff, food product, dietary supplement, or food additive according to the present invention, said process comprising admixing polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence with a feedstuff, food product, dietary supplement, food additive or ingredient thereof; optionally said polypeptide or polynucleotide is encapsulated in said process; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, a method for treating and/or preventing a disorder in a subject, wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide sequence or host cell treats and/or prevents a disorder in the subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, a method for modulating the inflammation of a tissue or an organ in a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide, polynucleotide sequence or host cell modulates the inflammation of a tissue or an organ in the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides a method for improving intestine barrier integrity in a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide sequence or host cell improves intestine barrier integrity in the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, a method for reducing the level of one or more types of lactose fermenting bacteria (such as E. coli) in a tissue or an organ in a subject and/or reducing the level of one or more types of non-lactose fermenting bacteria in a tissue or an organ in a subject, wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide, polynucleotide sequence or host cell reduces the level of one or more types of lactose fermenting bacteria (such as E. coli) in a tissue or an organ in the subject and/or reduces the level of one or more types of non-lactose fermenting bacteria in a tissue or an organ in the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, a method for maintaining the length of the large intestine and/or small intestine of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; (e.g. said subject has IBD); wherein said polypeptide or polynucleotide sequence or host cell maintains the length of the large intestine and/or small intestine of the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides a method for reducing disruption to the intestine (e.g. the large intestine) of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; (e.g. said subject has IBD); wherein said polypeptide or polynucleotide sequence or host cell reduces disruption to the intestine (e.g. large intestine) of the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, a method for regulating the expression of one or more pro-inflammatory or anti-inflammatory genes in a cell or cells of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide sequence or host cell regulates the expression of one or more pro-inflammatory genes and/or anti-inflammatory genes in a cell or cells of the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides a method for regulating the expression of one or more genes in a cell or cells of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, to said subject; wherein said polypeptide or polynucleotide sequence or host cell regulates the expression of one or more genes in a cell or cells of the subject; wherein the one or more genes are selected from the group consisting of regenerating islet-derived 3 beta gene (Reg3b), resistin-like gamma resistin like beta gene (RetnIg|Retnlb), sucrase-isomaltase (alpha-glucosidase) gene (Si), defensin alpha 24 gene (Defa24), hydroxysteroid 11-beta dehydrogenase 2 gene (Hsd11b2), hydroxysteroid (17-beta) dehydrogenase 2 gene (Hsd17b2), resistin-Like Molecule-beta (RELMb), and nuclear receptor 1D1 thyroid hormone receptor alpha gene (Nr1d1|Thra); (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, a method for reducing the activation of pro-inflammatory pathways in a cell or cells of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide sequence or host cell reduces the activation of pro-inflammatory pathways in a cell or cells of the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides a method for reducing the activity and/or expression of NF-κβ in a cell or cells (such as epithelial cells, epidermal cells, neuronal cells, and/or pancreatic cells) of a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide or host cell reduces the activity and/or expression of NF-κβ in a cell or cells (such as epithelial cells, epidermal cells, neuronal cells, and/or pancreatic cells) of the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides a method for improving alimentary canal health in a subject wherein said method comprises administering to the subject polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence; wherein said polypeptide or polynucleotide sequence or host cell improves alimentary canal health in the subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for the treatment and/or prevention of a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for modulating the inflammation of a tissue or an organ in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides use of polypeptide HP or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for improving intestine barrier integrity in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for maintaining the length of the large intestine and/or small intestine of a subject; (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides use of a polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for modifying the bacterial composition in a tissue or organ to provide a beneficial microbiota, preferably, for use in reducing the level of one or more types of lactose fermenting bacteria (such as E. coli) in a tissue or an organ in a subject and/or reducing the level of one or more types of non-lactose fermenting bacteria in a tissue or an organ in a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for reducing disruption to the intestine (e.g. large intestine) of a subject; (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in a further aspect, use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for regulating the expression of one or more pro-inflammatory genes in a cell or cells of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for regulating the expression in a cell or cells of a subject of one or more genes selected from the group consisting of regenerating islet-derived 3 beta gene (Reg3b), resistin-like gamma resistin like beta gene (RetnIg|Retnlb), sucrase-isomaltase (alpha-glucosidase) gene (Si), defensin alpha 24 gene (Defa24), hydroxysteroid 11-beta dehydrogenase 2 gene (Hsd11b2), hydroxysteroid (17-beta) dehydrogenase 2 gene (Hsd17b2), resistin-Like Molecule-beta (RELMb), and nuclear receptor 1D1 thyroid hormone receptor alpha gene (Nr1d1|Thra); (e.g. said subject has IBD); wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In another aspect, the present invention provides use of polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for reducing the activation of pro-inflammatory pathways in a cell or cells of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

In a further aspect, the present invention provides use of a polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for reducing the activity and/or expression of NF-κβ in a cell or cells (such as epithelial cells, epidermal cells, neuronal cells, and/or pancreatic cells) of a subject; wherein said polypeptide has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and wherein said polynucleotide sequence encodes a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof and/or wherein said polynucleotide sequence has at least 75% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof.

The present invention provides, in another aspect, use of a polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, for the manufacture of a medicament for improving alimentary canal health in a subject.

FIGURES

The invention is described with reference to the accompanying figures, wherein:

FIG. 1A shows an alignment of the polynucleotide sequences encoding HP (SEQ ID NO 1), E. coli optimised HP (Rec 1 HP—SEQ ID NO 3) and L. lactis optimised HP (Rec 2 HP—SEQ ID NO 5). HP is deposited with GenBank under accession number: AAO75294.1 and is described in GenBank as possible Pirin family protein [Bacteroides thetaiotaomicron VPI-5482].

FIG. 1B shows an alignment of the polypeptide sequences HP (SEQ ID NO 2), E. coli optimised HP (Rec 1 HP—SEQ ID NO 4) and L. lactis optimised HP (Rec 2 HP—SEQ ID NO 6). HP is deposited with GenBank under accession number: AAO75294.1 and is described in GenBank as possible Pirin family protein [Bacteroides thetaiotaomicron VPI-5482].

FIG. 2A shows the change in weight in rats given Dextran Sodium Sulphate (DSS) in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 2B shows the change in water intake by rats given Dextran Sodium Sulphate (DSS) in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 2C shows the change in food intake by rats given Dextran Sodium Sulphate (DSS) in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 3 shows the length of the colon and small intestine in rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 4 shows the numbers of lactose-fermenting (predominantly E. coli) and non-lactose-fermenting bacteria in tissues from rats given Dextran Sodium Sulphate (DSS) in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP). [When Log 10=1.0, no bacteria were detected].

FIG. 5A shows the morphology of the descending colon from rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 5B shows the morphology of the ascending colon from rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 6 shows the mean histopathology scores and histopathology scores as percentage fields of view with pathology of grades 0-3 for the ascending colon from rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 7 shows the heatmap of 377 differentially expressed genes in tissue from rats given Dextran Sodium Sulphate in water with or without co-treatment with hypothetical protein (HP).

FIG. 8A shows the expression of inflammation-associated genes (Realtime PCR) in ascending colons from rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

FIG. 8B shows the expression of inflammation-associated genes (Realtime PCR) in ascending colons from rats given Dextran Sodium Sulphate in water with (DSS/HP) or without (DSS) co-treatment with hypothetical protein (HP).

DETAILED DESCRIPTION HP

Without wishing to be bound by theory, the polypeptide HP of the present invention is a pirin-related protein.

Polypeptide HP has at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identity to the polypeptide sequence shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof.

One example of polypeptide HP of the present invention is SEQ ID NO 2 deposited with GenBank as AAO75294.1; Bacteroides thetaiotaomicron comprising SEQ ID NO 1 can be found deposited as DSM2079 [E50(VP15482), VP15482] at DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH). The polypeptide sequence SEQ ID NO 2 has the following sequence:

        10         20         30         40   MKKVIDRASS RGYFNHGWLK THHTFSFANY YNPERIHFGA          50         60         70         80  LRVLNDDSVD PSMGFDTHPH KNMEVISIPL KGYLRHGDSV          90        100        110        120  QNTKTITPGD IQVMSTGSGI YHSEYNDSKE EQLEFLQIWV          130        140        150        160  FPRIENTKPE YNNFDIRPLL KPNELSLFIS PNGKTPASIK          170        180        190        200 QDAWFSMGDF DTERTIEYCM HQEGNGAYLF VIEGEISVAD        210        220        230  EHLAKRDGIG IWDTKSFSIR ATKGTKLLVM EVPM 

AAO75294.1 is described as being a possible Pirin family protein. AAO75294.1 was identified from Bacteroides thetaiotaomicron VPI-5482.

The polypeptides sequences deposited in GenBank as AAO76683.1 and CDE80552.1 are examples of polypeptides having at least 75% identity to SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6.

The polypeptide sequence of AAO76683.1 is as follows:

        10         20         30         40  MKKVIHKADT RGHSQYDWLD SYHTFSFDEY FDSDRINFGA          50         60         70         80  LRVLNDDKVA PGEGFQTHPH KNMEIISIPL KGHLQHGDSK           90        100        110        120  KNSRIITVGE IQTMSAGTGI FHSEVNASPV EPVEFLQIWI          130        140        150        160  MPRERNTHPV YKDFSIKELE RPNELAVIVS PDGSTPASLL         170        180        190        200  QDTWFSIGKV EAGKKLGYHL HQSHGGVYIF LIEGEIVVDG         210        220        230  EVLKRRDGMG VYDTKSFELE TLKDSHILLI EVPM 

The polypeptide sequence of AAO76683.1 is also referred to as SEQ ID NO 7 herein. AAO76683.1 is described in GenBank as being a putative Pirin family protein. AAO76683.1 was isolated from Bacteroides thetaiotaomicron VPI-5482. [E50(VP15482), VP15482]. Bacteroides thetaiotaomicron comprising SEQ ID NO 7 can be found deposited as DSM2079 BT 1576 at DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH).

The polypeptide sequence of CDE80552.1 is as follows:

        10         20         30         40  MKKVIHKADT RGHSQYDWLD SYHTFSFDEY FDSDRINFGA           50         60         70         80  LRVLNDDKVA PGEGFQTHPH KNMEIISIPL KGHLQHGDSK           90        100        110        120  KNSRIITVGE IQTMSAGTGI FHSEVNASPV EPVEFLQIWI        130        140        150        160  MPRERNTHPV YKDFSIKELE RPNELAVIVS PDGSTPASLL          170        180        190        200  QDTWFSIGKV EAGKKLGYHL HQSHGGVYIF LIEGEIVVDG          210        220        230  EVLKRRDGMG VYDTKSFELE TLKDSHILLI EVPM

The polypeptide sequence of CDE80552.1 is also referred to as SEQ ID NO 8 herein. CDE80552.1 is described in GenBank as being a putative Pirin family protein. CDE80552.1 was isolated from Bacteroides thetaiotaomicron CAG:40.

The terms “polypeptide HP”, “HP polypeptide” and “HP” are used interchangeably herein.

In one embodiment, the polypeptide HP is the polypeptide shown as SEQ ID NO 2.

In another embodiment, the polypeptide HP is the polypeptide shown as SEQ ID NO 4.

In further embodiment, the polypeptide HP is the polypeptide shown as SEQ ID NO 6.

HP polypeptides can be derived from certain microorganisms. In one aspect, the HP polypeptide is derived from an anaerobic, gram negative bacterium which can live in the alimentary canal. In a further aspect, the HP polypeptide is derived from a Bacteroides spp such as a Bacteroides thetaiotaomicron.

Examples of a polynucleotide sequence encoding polypeptide HP include the polynucleotide sequences shown as SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5; polynucleotide sequences encoding the polypeptide shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6; polynucleotides sequences having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or variants, homologues, fragments or derivatives thereof; polynucleotides sequences encoding a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polypeptide shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or variants, homologues, fragments or derivatives thereof; and polynucleotide sequences encoding SEQ ID NO 7 or SEQ ID NO 8.

SEQ ID NOs 1, 3 and 5 are shown in FIG. 1A.

SEQ ID NO 1 has the following sequence:

Atgaaaaaagtaatcgacagagcttcatcaagaggctattttaatcatgg ctggctcaaaacccaccacacattcagttttgctaactattacaatccgg aaagaatccatttcggagccttgcgagtgctgaatgatgacagtgtagac ccgtcgatgggatttgatactcatccacataaaaatatggaagtaatttc cattccgttgaaagggtatctgagacatggcgacagtgtacaaaatacga aaacgattactcccggtgatatccaagtgatgagtacgggcagtggtatc tatcatagtgagtataacgacagcaaggaagaacaattggaattcctgca aatatgggtattcccccgaatcgagaatacgaaacccgaatataacaatt tcgatatacgtccgctgctgaaaccgaacgagttatctctgttcatttca ccgaacggcaagacaccggcctccatcaaacaggatgcctggttctctat gggagacttcgatacggaaagaaccatcgaatattgtatgcatcaggaag gtaacggagcttatctgtttgtgatagaaggagagatcagcgtggccgat gaacatctggccaaacgtgacggcatcggaatatgggataccaaaagctt ctctatccgtgctactaaagggaccaaacttctggtaatggaagtaccca tgtaa 

SEQ ID NO 1 encodes SEQ ID NO 2 which is deposited with GenBank under accession number AAO75294.1.

The polynucleotide sequence of SEQ ID NO 1 was codon optimised for expression in E. coli. This codon optimised sequence is shown as SEQ ID NO 3. This sequence may also be referred herein as “Rec 1 HP” or “recombinant 1 HP”.

SEQ ID NO 3 has the following sequence:

ggtaccatgaaaaaagtgattgatcgtgcgagcagccgtggctattttaa ccatggctggctgaaaacccatcatacctttagcttcgcgaactattata atccggaacgcattcattttggcgcgctgcgtgtgctgaacgatgatagc gtggatccgagcatgggctttgatacccatccgcacaaaaacatggaagt gattagcattccgctgaaaggctatctgcgtcatggcgatagcgtgcaga acaccaaaaccattaccccgggtgatattcaggtgatgagcaccggcagc ggcatttatcatagcgaatacaacgatagcaaagaagaacagctggaatt tctgcagatttgggtgtttccgcgtattgaaaacaccaaaccggaatata acaactttgatattcgcccgctgctgaaaccgaacgaactgagcctgttt attagcccgaacggcaaaaccccggcgagcattaaacaggatgcgtggtt tagcatgggcgattttgataccgaacgcaccattgaatattgcatgcatc aggaaggcaacggcgcgtacctgtttgtgattgaaggcgaaattagcgtg gcggatgaacatctggccaaacgtgatggcattggcatttgggataccaa aagcttcagcattcgtgcgaccaaaggcaccaaactgctggtgatggaag tgccgatgtaataagagctc 

The polypeptide sequence encoded by SEQ ID NO 3 is shown as SEQ ID NO 4. SEQ ID NO 4 has the following sequence:

GTMKKVIDRASSRGYFNHGWLKTHHTFSFANYYNPERIHFGALRVLNDDS VDPSMGFDTHPHKNMEVISIPLKGYLRHGDSVQNTKTITPGDIQVMSTGS GIYHSEYNDSKEEQLEFLQIWVFPRIENTKPEYNNFDIRPLLKPNELSLF ISPNGKTPASIKQDAWFSMGDFDTERTIEYCMHQEGNGAYLFVIEGEISV ADEHLAKRDGIGIWDTKSFSIRATKGTKLLVMEVPM EL 

The polynucleotide sequence of SEQ ID NO 1 was codon optimised for expression in Lactococcus lactis. This codon optimised sequence is shown as SEQ ID NO 5. This sequence may also be referred herein as “Rec 2 HP” or “recombinant 2 HP”.

SEQ ID NO 5 has the following sequence:

ggtaccatgaaaaaagttattgatcgtgcttcatcacgtggatattttaa tcatggatggcttaaaactcatcatacatttagttttgccaattattata atccagaacgtattcattttggtgctcttcgtgttcttaatgatgattca gttgatccatcaatgggatttgatacacatccacataaaaatatggaagt tatttcaattccacttaaaggatatcttcgtcatggtgattcagttcaaa atacaaaaacaattacacctggagatattcaagttatgtctacaggatca ggaatttatcattcagaatataatgattcaaaagaagaacaacttgaatt tcttcaaatttgggtctttccacgtattgaaaatacaaaaccagaatata ataatttcgacattcgtccacttcttaaaccaaatgaactttcacttttt atctcaccaaatggaaaaacaccagcttcaattaaacaagatgcttggtt ttcaatgggagattttgatacagaacgtacaattgaatattgtatgcatc aagaaggtaacggcgcttatctttttgttattgaaggtgaaatttcagtt gctgatgaacatcttgctaaacgtgatggaattggaatttgggatacaaa atcattttcaattcgtgctacaaaaggtacaaaacttcttgttatggaag ttccaatgtaataagagctc 

The polypeptide sequence encoded by SEQ ID NO 5 is shown as SEQ ID NO 6. SEQ ID NO 6 has the following sequence:

GTMKKVIDRASSRGYFNHGWLKTHHTFSFANYYNPERIHFGALRVLNDDS VDPSMGFDTHPHKNMEVISIPLKGYLRHGDSVQNTKTITPGDIQVMSTGS GIYHSEYNDSKEEQLEFLQIWVFPRIENTKPEYNNFDIRPLLKPNELSLF ISPNGKTPASIKQDAWFSMGDFDTERTIEYCMHQEGNGAYLFVIEGEISV ADEHLAKRDGIGIWDTKSFSIRATKGTKLLVMEVPM EL 

In one embodiment, the polynucleotide sequence encoding polypeptide HP has at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polynucleotide sequence shown as SEQ ID NO 1, SEQ ID NO 3 or SEQ ID NO 5 or to variants, homologues, fragments or derivatives thereof.

In one embodiment, the polynucleotide sequence encoding polypeptide HP encodes a polypeptide shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polypeptide shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6 or to variants, homologues, fragments or derivatives thereof.

In one embodiment, the polypeptide HP is a truncated HP polypeptide. For example, the truncated polypeptide comprises at least 20, 30, 40, 50, 75, 100, 125, 150, 175 or 200 amino acids of polypeptide shown as SEQ ID NO 2, SEQ ID NO 4 or SEQ ID NO 6.

In one embodiment, the polynucleotide sequence encoding the polypeptide HP encodes a truncated HP polypeptide.

In one embodiment, the polypeptide HP is a fusion polypeptide. For example, the polypeptide is fused to glutathione S-transferase (GST).

Host Cell

In one aspect, a host cell as described herein comprises a polynucleotide sequence encoding polypeptide HP.

In another aspect, a host cell as described herein comprises an expression vector comprising a polynucleotide sequence encoding polypeptide HP.

In a further aspect, a host cell as described herein has been transformed with a nucleotide sequence that causes the host cell to overexpress HP. For example, a promoter is inserted into the genome of a host cell which enables the host cell to overexpress a polynucleotide sequence HP (such as an endogenous polynucleotide sequence)—i.e. the promoter is capable of overexpressing the polynucleotide sequence encoding HP.

As used herein, the term “overexpress” in the phrase “a nucleotide sequence that causes the host cell to overexpress HP” and “promoter capable of overexpressing the polynucleotide sequence encoding HP” refers to an increase in expression from zero to a level of expression or going from a lower level of expression to a higher level of expression (e.g. upregulation) when the transformed host cell is compared to the equivalent host cell prior to transformation.

In one embodiment, the level of mRNA encoding HP in a transformed host cell which overexpresses HP is increased (i.e. upregulated) such that the level of mRNA is at least 10%, 20%, 30%, 40% or 50% higher in a transformed host cell when compared to the equivalent host cell prior to transformation.

Examples of host cells overexpressing HP include: (i) host cells transformed with an expression vector encoding HP (prior to transformation said host cell was not capable of expressing HP); and (ii) host cells transformed to upregulate the expression of an endogenous HP (prior to transformation said host cell was capable of expressing said HP for a given set of culture conditions but after transformation said host cell is capable of expressing said HP at a higher level, in the same culture conditions).

The polynucleotide sequence encoding polypeptide HP may be codon optimised for the host cell. For instance, the polypeptide sequence may be codon optimised for expression in E. coli (such as SEQ ID NO 3) or the polynucleotide sequence may be codon optimised for expression in Lactococcus lactis (such as SEQ ID NO 5).

The term “host cell”—in relation to the present invention—includes any cell that comprises either the polynucleotide sequence encoding HP as described herein or an expression vector comprising said polynucleotide sequence as described herein. The host cell may be used in the recombinant production of a protein having the specific properties as defined herein. The host cell may contain a heterologous polynucleotide sequence coding for HP or may be a cell expressing its natural HP polynucleotide. For example, the host cell may be from Bacteroides spp such as Bacteroides thetaiotaomicron.

The term “host cell” as used herein may be interchangably used with “host organism” and “host microorganism”.

Thus, there is provided host cells transformed or transfected with a polynucleotide sequence encoding HP as described herein or an expression vector comprising said polynucleotide sequence as described herein.

The term “transfected cell” or “transfected host cell” as used herein means a host cell transfected so that it comprises a polynucleotide sequence encoding HP as described herein or an expression vector comprising said polynucleotide sequence as described herein. In addition or alternatively, the host cell has been transformed with a nucleotide sequence that causes the host cell to overexpress a polynucleotide sequence encoding HP. For example, a promoter is inserted into the genome of a host cell which enables the host cell to overexpress an endogenous poly nucleotide sequence encoding HP.

The term “transformed cell” or “transformed host cell” as used herein means a host cell having a modified genetic structure.

The term “host cell” includes any cell which a vector is capable of transfecting or transducing.

Host cells will be chosen to be compatible with the vector and may for example be prokaryotic (for example bacterial), fungal, yeast or plant cells.

Host cells comprising polynucleotide sequences encoding polypeptide HP or an expression vector comprising said polynucleotide sequence may be used to express the polypeptide HP under in vitro, in vivo and ex vivo conditions.

In one embodiment, the host cell is a microorganism, such as a bacterium. Typically, the microorganism which inhabits the alimentary canal, or a section of the alimentary canal. Examples of suitable bacterial host cells are gram positive or gram negative bacterial species. For instance, the host cell may be selected from the group consisting of Bacteroides spp (such as Bacteroides thetaiotaomicron), E. coli, Lactococcus spp (such as L. lactis), Lactobacillus spp, Bifidobacterium spp, and Streptococcus spp (such as Streptococcus thermophilus).

In one embodiment, the host cell comprises an exogenous polynucleotide sequence encoding HP.

In another embodiment, the host cell comprises an endogenous polynucleotide sequence encoding HP. For example, the endogenous polynucleotide sequence under the control of a non-native promoter (such as a constitutive promoter). In a further example, the host cell comprises multiple copies of the endogenous polynucleotide sequence.

The term “host cell” does not cover native nucleotide coding sequences in their natural environment when they are under the control of their native promoter which is also in its natural environment. An example of a host cell which has a native nucleotide sequence which is not in its natural environment is a Bacteroides thetaiotaomicron VPI-5482 comprising SEQ ID NO 1 in which SEQ ID NO 1 under the control of a non-native promoter (such as a constitutive promoter). In another example, a Bacteroides thetaiotaomicron VPI-5482 comprising SEQ ID NO 1 has multiple copies of SEQ ID NO 1.

Depending on the nature of the nucleotide sequence, and/or the desirability for further processing of the expressed protein, eukaryotic hosts such as yeasts or other fungi or insect cells (such as insect Sf9 cells) may be used. In general, yeast cells are preferred over fungal cells because they are easier to manipulate. However, some proteins are either poorly secreted from the yeast cell, or in some cases are not processed properly (e.g. hyperglycosylation in yeast). In these instances, a different fungal host organism should be selected.

The use of suitable host cells—such as yeast, fungal and plant host cells—may provide for post-translational modifications (e.g. myristoylation, glycosylation, truncation, lapidation and tyrosine, serine or threonine phosphorylation) as may be needed to confer optimal biological activity on the polypeptide described herein.

Host cells may be cultured under suitable conditions which allow expression of the polypeptide.

In some embodiments, the polypeptide can be extracted from host cells by a variety of techniques known in the art, including enzymatic, chemical and/or osmotic lysis and physical disruption. The polypeptide may be purified and isolated in a manner known per se.

Transformation of Host Cells

Teachings on the transformation of prokaryotic hosts is well documented in the art, for example see Sambrook et al (Molecular Cloning: A Laboratory Manual, 2nd edition, 1989, Cold Spring Harbor Laboratory Press). If a prokaryotic host is used then the nucleotide sequence may need to be suitably modified before transformation—such as by removal of introns.

Filamentous fungi cells may be transformed using various methods known in the art—such as a process involving protoplast formation and transformation of the protoplasts followed by regeneration of the cell wall in a manner known. The use of Aspergillus as a host microorganism is described in EP 0 238 023.

Another host organism can be a plant. A review of the general techniques used for transforming plants may be found in articles by Potrykus (Annu Rev Plant Physiol Plant Mol Biol [1991] 42:205-225) and Christou (Agro-Food-Industry Hi-Tech March/April 1994 17-27). Further teachings on plant transformation may be found in EP-A-0449375.

General teachings on the transformation of fungi, yeasts and plants are presented in following sections.

Transformed Fungus

A host cell may be a fungus—such as a mould. Examples of suitable such hosts include any member belonging to the genera Thermomyces, Acremonium, Aspergillus, Penicillium, Mucor, Neurospora, Trichoderma and the like.

In one embodiment, the host cell may be a filamentous fungus.

Transforming filamentous fungi is discussed in U.S. Pat. No. 5,741,665 which states that standard techniques for transformation of filamentous fungi and culturing the fungi are well known in the art. An extensive review of techniques as applied to N. crassa is found, for example in Davis and de Serres, Methods Enzymol (1971) 17A: 79-143.

Further teachings which may also be utilised in transforming filamentous fungi are reviewed in U.S. Pat. No. 5,674,707.

In addition, gene expression in filamentous fungi is taught in in Punt et al. (2002) Trends Biotechnol 2002 May; 20(5):200-6, Archer & Peberdy Crit Rev Biotechnol (1997) 17(4):273-306.

The present description encompasses the production of transgenic filamentous fungi according to the present description prepared by use of these standard techniques.

In one aspect, the host organism can be of the genus Aspergillus, such as Aspergillus niger.

A transgenic Aspergillus according to the present invention can also be prepared by following, for example, the teachings of Turner G. 1994 (Vectors for genetic manipulation. In: Martinelli S. D., Kinghorn J. R. (Editors) Aspergillus: 50 years on. Progress in industrial microbiology vol 29. Elsevier Amsterdam 1994. pp. 641-666).

Transformed Yeast

In another embodiment, the transgenic organism can be a yeast.

A review of the principles of heterologous gene expression in yeast are provided in, for example, Methods Mol Biol (1995), 49:341-54, and Curr Opin Biotechnol (1997) October; 8(5):554-60

In this regard, yeast—such as the species Saccharomyces cerevisi or Pichia pastoris (see FEMS Microbiol Rev (2000 24(1):45-66), may be used as a vehicle for heterologous gene expression.

A review of the principles of heterologous gene expression in Saccharomyces cerevisiae and secretion of gene products is given by E Hinchcliffe E Kenny (1993, “Yeast as a vehicle for the expression of heterologous genes”, Yeasts, Vol 5, Anthony H Rose and J Stuart Harrison, eds, 2nd edition, Academic Press Ltd.).

For the transformation of yeast, several transformation protocols have been developed. For example, a transgenic Saccharomyces according to the present invention can be prepared by following the teachings of Hinnen et al., (1978, Proceedings of the National Academy of Sciences of the USA 75, 1929); Beggs, J D (1978, Nature, London, 275, 104); and Ito, H et al (1983, J Bacteriology 153, 163-168).

The transformed yeast cells may be selected using various selective markers—such as auxotrophic markers dominant antibiotic resistance markers.

Transformed Plants/Plant Cells

A host cell suitable for the present invention may be a plant. In this respect, the basic principle in the construction of genetically modified plants is to insert genetic information in the plant genome so as to obtain a stable maintenance of the inserted genetic material. A review of the general techniques may be found in articles by Potrykus (Annu Rev Plant Physiol Plant Mol Biol [1991] 42:205-225) and Christou (Agro-Food-Industry Hi-Tech March/April 1994 17-27).

Direct infection of plant tissues by Agrobacterium is a simple technique which has been widely employed and which is described in Butcher D. N. et al., (1980), Tissue Culture Methods for Plant Pathologists, eds.: D. S. Ingrams and J. P. Helgeson, 203-208.

Other techniques for transforming plants include ballistic transformation, the silicon whisker carbide technique (see Frame B R, Drayton P R, Bagnaall S V, Lewnau C J, Bullock W P, Wilson H M, Dunwell J M, Thompson J A & Wang K (1994) Production of fertile transgenic maize plants by silicon carbide whisker-mediated transformation, The Plant Journal 6: 941-948) and viral transformation techniques (e.g. see Meyer P, Heidmann I & Niedenhof I (1992) The use of cassava mosaic virus as a vector system for plants, Gene 110: 213-217).

Further teachings on plant transformation may be found in EP-A-0449375.

Plant cells may be grown and maintained in accordance with well-known tissue culturing methods such as by culturing the cells in a suitable culture medium supplied with the necessary growth factors such as amino acids, plant hormones, vitamins, etc.

In a further aspect, the present description relates to a vector system which carries a nucleotide sequence or construct according to the present description and which is capable of introducing the nucleotide sequence or construct into the genome of an organism, such as a plant. The vector system may comprise one vector, but it may comprise two vectors. In the case of two vectors, the vector system is normally referred to as a binary vector system. Binary vector systems are described in further detail in Gynheung An et al., (1980), Binary Vectors, Plant Molecular Biology Manual A3, 1-19.

One extensively employed system for transformation of plant cells uses the Ti plasmid from Agrobacterium tumefaciens or a Ri plasmid from Agrobacterium rhizogenes An et al., (1986), Plant Physiol. 81, 301-305 and Butcher D. N. et al., (1980), Tissue Culture Methods for Plant Pathologists, eds.: D. S. Ingrams and J. P. Helgeson, 203-208. After each introduction method of the desired promoter or construct or nucleotide sequence according to the present invention in the plants, the presence and/or insertion of further DNA sequences may be necessary. If, for example, for the transformation the Ti- or Ri-plasmid of the plant cells is used, at least the right boundary and often however the right and the left boundary of the Ti- and Ri-plasmid T-DNA, as flanking areas of the introduced genes, can be connected. The use of T-DNA for the transformation of plant cells has been intensively studied and is described in EP-A-120516; Hoekema, in: The Binary Plant Vector System Offset-drukkerij Kanters B. B., Alblasserdam, 1985, Chapter V; Fraley, et al., Crit. Rev. Plant Sci., 4:1-46; and An et al., EMBO J. (1985) 4:277-284.

Culturing and Production

Host cells transformed with the nucleotide sequence described herein may be cultured under conditions conducive to the production of the encoded polypeptide and which facilitate recovery of the polypeptide from the cells and/or culture medium.

The medium used to cultivate the cells may be any conventional medium suitable for growing the host cell in questions and obtaining expression of the polypeptide.

The protein produced by a recombinant cell may be displayed on the surface of the cell.

The protein may be secreted from the host cells and may conveniently be recovered from the culture medium using well-known procedures.

Secretion

Often, it is desirable for the protein to be secreted from the expression host cell into the culture medium from where the protein may be more easily recovered. According to the present description, the secretion leader sequence may be selected on the basis of the desired expression host. Hybrid signal sequences may also be used with the context of the present invention.

Typical examples of heterologous secretion leader sequences are those originating from the fungal amyloglucosidase (AG) gene (glaA—both 18 and 24 amino acid versions e.g. from Aspergillus), the a-factor gene (yeasts e.g. Saccharomyces, Kluyveromyces and Hansenula) or the a-amylase gene (Bacillus).

By way of example, the secretion of heterologous proteins in E. coli is reviewed in Methods Enzymol (1990) 182:132-43.

Expression Vectors

The term “expression vector” means a construct capable of in vivo, ex vivo or in vitro expression.

The term “construct”—which is synonymous with terms such as “conjugate”, “cassette” and “hybrid”—includes a nucleotide sequence as described herein which optionally may be directly or indirectly attached to a promoter. An example of an indirect attachment is the provision of a suitable spacer group such as an intron sequence, such as the Sh1-intron or the ADH intron, intermediate the promoter and the nucleotide sequence of the present invention. The same is true for the term “fused” in relation to the present invention which includes direct or indirect attachment. In some cases, the terms do not cover the natural combination of the nucleotide sequence coding for the protein ordinarily associated with the wild type gene promoter and when they are both in their natural environment.

The construct may even contain or express a marker, which allows for the selection of the genetic construct.

For some applications, the construct comprises at least the nucleotide sequence described herein operably linked to a promoter.

The nucleotide sequence of the present description may be present in a vector in which the nucleotide sequence is operably linked to regulatory sequences capable of providing for the expression of the nucleotide sequence by a suitable host cell.

In some embodiments, the polynucleotide sequence encoding polypeptide HP of an expression vector may be codon optimised for the host cell which will be or has been transformed or transfected with the polynucleotide sequence.

The term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A regulatory sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under condition compatible with the control sequences. For example, a promoter is operably linked to a coding sequence if it controls the transcription of the coding sequence.

The term “regulatory sequences” includes promoters and enhancers and other expression regulation signals.

The term “promoter” is used in the normal sense of the art, e.g. an RNA polymerase binding site. The promoter may be heterologous or homologous to the nucleotide sequence.

Enhanced expression of the nucleotide sequence described herein may also be achieved by the selection of heterologous regulatory regions, e.g. promoter, secretion leader and terminator regions.

In one embodiment, the nucleotide sequence as described herein is operably linked to at least a promoter.

Other promoters may even be used to direct expression of the polypeptide described herein.

Examples of suitable promoters for directing the transcription of the nucleotide sequence in a bacterial, fungal or yeast host are well known in the art.

The promoter can additionally include features to ensure or to increase expression in a suitable host. For example, the features can be conserved regions such as a Pribnow Box or a TATA box.

Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, be incorporated into the genome into the genome of a suitable host cell. In some instances, the term “incorporated” covers stable incorporation into the genome.

The vectors for use in the present invention may be transformed into a suitable host cell as described herein to provide for expression of a polypeptide of the present description.

The vector may be a plasmid, a phage particle, or simply a potential genomic insert.

The choice of vector e.g. a plasmid, cosmid, or phage vector will often depend on the host cell into which it is to be introduced.

The vectors for use in the present invention may contain one or more selectable marker genes-such as a gene, which confers antibiotic resistance e.g. ampicillin, kanamycin, chloramphenicol or tetracyclin resistance. Alternatively, the selection may be accomplished by co-transformation (as described in WO91/17243).

Vectors may be used in vitro, for example for the production of RNA or used to transfect, transform, transduce or infect a host cell.

The vector may further comprise a nucleotide sequence enabling the vector to replicate in the host cell in question. Examples of such sequences are the origins of replication of plasmids pUC19, pACYC177, pUB110, pE194, pAMB1 and pIJ702.

In one embodiment, an expression vector comprises one or more polynucleotide sequences according to the present invention. The polynucleotide sequence may be heterologous or homologous to a host cell transformed or transfected with the expression vector.

Disorders

Polypeptide HP or a polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence may be used for the treatment and/or prevention of a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder. The disorder may also be of the CNS, including autism.

In one embodiment, the disorder affects the alimentary canal, a section of the alimentary canal, the liver, liver cells, epithelial cells, epidermal cells, neuronal cells, the pancreas, and/or pancreatic cells (such as the islets of Langerhans), kidneys, spleen, lungs and heart and/or cells thereof.

Examples of sections (i.e. parts) of the alimentary canal include the mouth, the oesophagus, the stomach and the intestine (such as the small intestine (e.g. the duodenum, the jejunum and the ileum) and/or the large intestine (e.g. the caecum, ascending colon, transverse colon, descending colon, and sigmoid colon)).

Examples of epithelial cells include intestinal, oral, lung, nasal, vaginal epithelial cells.

In one embodiment, the disorder is selected from the group consisting of inflammatory bowel disorder (IBD), colitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, coeliac disease, atopic dermatitis, rhinitis, irritable bowel syndrome (IBS), ulcerative colitis, pouchitis, Crohn's disease, functional dyspepsia, atopic diseases, necrotising enterocolitis, non alcoholic fatty liver disease, gastrointestinal infection, Lupus, nephritis/glomerulonephritis, asthma, COPD, mycocarditis and combinations thereof.

In one aspect, the disorder affects the intestine.

In one aspect, the disorder is an inflammatory disorder. For example, the disorder is an inflammatory bowel disorder (IBD) such as Crohn's disease.

In one aspect, the disorder is an autoimmune disorder. For example, the autoimmune disorder is selected from the group consisting of ulcerative colitis, pouchitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, allergies (including coeliac disease), atopic dermatitis, rhinitis, Lupus, nephritis/glomerulonephritis, asthma, COPD and mycocarditis.

Subject

In one embodiment, the subject is a monogastric animal.

Examples of monogastric animals include poultry, humans, rats, pigs, dogs, cats, horses and rabbits.

In another embodiment, the subject is a mammal such as a monogastric mammal.

Examples of monogastric mammals include omnivores (such as humans, rats, and pigs), carnivores (such as dogs and cats), and herbivores (such as horses and rabbits).

In one embodiment, the subject is a human.

In one aspect, the subject has a disorder is selected from the group consisting of inflammatory bowel disorder (IBD), colitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, coeliac disease, atopic dermatitis, rhinitis, irritable bowel syndrome (IBS), ulcerative colitis, pouchitis, Crohn's disease, functional dyspepsia, atopic diseases, necrotising enterocolitis, non alcoholic fatty liver disease, gastrointestinal infection Lupus, nephritis/glomerulonephritis, asthma, COPD, mycocarditis and combinations thereof. For example, the subject has IBD.

Modulation/Regulation

The terms “modulation” and “regulation” may be used interchangeably herein.

In one embodiment polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to modulate the inflammation of a cell, a tissue or an organ in a subject.

In one embodiment, the term “modulation” refers to an increase and/or induction and/or promotion and/or activation. In an alternative embodiment, the term “modulation” refers to a decrease and/or reduction and/or inhibition.

In one embodiment, the term “regulation” refers to an upregulation. In an alternative embodiment, the term “regulation” refers to a downregulation.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein reduces the inflammation of a cell, a tissue or an organ. For example, inflammation of the alimentary canal, a section (i.e. part) of the alimentary canal (such as the intestine), the liver, liver cells, epithelial cells, epidermal cells, neuronal cells, the pancreas, and/or pancreatic cells (such as the islets of Langerhans), kidneys, spleen, lungs and heart and/or cells thereof is reduced.

In one example, inflammation of the alimentary canal or part thereof (such as the intestine) is reduced.

In another example, inflammation by epithelial cells of the tissue or the organ is reduced.

The term “inflammation” as used herein refers to one or more of the following: redness, swelling, pain, tenderness, heat, and disturbed function of a cell, a tissue or organ due to an inflammatory process triggered by over-reaction of the immune system.

In one embodiment, the numbers of cells which are inflamed in a subject is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of cells which are inflamed in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or a host cell as described herein is administered to the subject.

In one embodiment, the amount of a tissue or organ which is inflamed in a subject is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the amount of tissue or organ which is inflamed in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or a host cell as described herein is administered to the subject.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cells as described herein reduces the inflammation by epithelial cells of the tissue or the organ.

For example, the epithelial cells are epithelial cells of the alimentary canal or part thereof (such as the intestine).

Without wishing to be bound by theory, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein increases the production of T cells (such as regulatory T cells which may also be referred to as Tregs) in a subject. This increase in Treg numbers may combat the effects of other effector T cells (also referred to as Teffs), such as Th1, Th17 and Th2 which drive inflammation, autoimmunity and allergic/atopic conditions. In Crohn's disease and ulcerative colitis the Teff/Treg cell balance is lost.

In one embodiment, the production of T cells in a subject is increased such that there are at least 10%, 20%, 30%, 40% or 50% more T cells, or greater than 100% more T cells after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the number of T cells in the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Intestine Barrier Integrity

In one embodiment, the polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to improve intestine barrier integrity in a subject.

The term “improving intestine barrier integrity” as used herein refers to a reduction in the numbers and/or types of microorganisms which spread from the intestine into other cells in a subject after administration of the polypeptide or polynucleotide or host cells as described herein when compared to the numbers and/or types of microorganisms which spread from the intestine into other cells in a subject before administration of the polypeptide or polynucleotide or host cell as described herein.

In one embodiment, the numbers of microorganisms which spread from the intestine into other cells in a subject are at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of microorganisms which spread from the intestine into other cells in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, there are at least 5%, 10%, 15% or 20% fewer types of microorganisms which spread from the intestine into other cells in a subject after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the types of microorganisms which spread from the intestine into other cells in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or a host cell as described herein is administered to the subject.

Levels of Bacteria

In one embodiment polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to modify the bacterial composition in a tissue or organ to provide a more beneficial microbiota. For example, the invention can be used to reduce the level of one or more types of lactose fermenting bacteria (such as E. coli) in a tissue or an organ in a subject and/or reduce the level of one or more types of non-lactose fermenting bacteria in a tissue or an organ in a subject.

The term “reduce the level of one or more types of lactose fermenting bacteria” as used herein refers to a reduction in the numbers of lactose fermenting bacteria in a tissue or organ in a subject after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of lactose fermenting bacteria in a tissue or organ in a subject before administration of the polypeptide or polynucleotide or host cell as described herein.

In one embodiment, the numbers of lactose fermenting bacteria in a tissue or organ in a subject are at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of lactose fermenting bacteria in a tissue or organ in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Examples of lactose fermenting bacteria include E. coli, Enterobacter and Klebsiella.

The term “reduce the level of one or more types of non-lactose fermenting bacteria” as used herein refers to a reduction in the numbers of non-lactose fermenting bacteria in a tissue or organ in a subject after administration of the polypeptide or polynucleotide or host cells when compared to the numbers of non-lactose fermenting bacteria in a tissue or organ in a subject before administration of the polypeptide or polynucleotide or host cell as described herein.

In one embodiment, the numbers of non-lactose fermenting bacteria in a tissue or organ in a subject are at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of non-lactose fermenting bacteria in a tissue or organ in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Examples of non-lactose fermenting bacteria include as Salmonella, Proteus species, Pseudomonas aeruginosa and Shigella.

In one embodiment the tissue or organ is selected from the group consisting of mesenteric lymph nodes, liver, pancreas, spleen and combinations thereof.

Regulating Appetite and/or Weight

In one embodiment, polypeptide HP or a polynucleotide sequence encoding said polypeptide or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence is used to regulate the appetite (e.g. food intake) in a subject (such as a subject with IBD).

As used herein, the term “regulate appetite” or “regulating appetite” refers to the ability to modulate (e.g. increase or decrease) the desire for a subject to eat food.

In one embodiment, the term “regulate” or “regulation” refers to an increase in appetite (e.g. food intake). In an alternative embodiment, the term “regulate” or “regulation” refers to a decrease in appetite (e.g. food intake).

For example, the polypeptide or polynucleotide or host cell as described herein maintains or stimulates the appetite in the subject.

In one embodiment, polypeptide HP or a polynucleotide sequence encoding said polypeptide or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence is used to regulate the weight of a subject (such as a subject with IBD).

In one embodiment, the term “regulate” or “regulation” refers to an increase in weight. In an alternative embodiment, the term “regulate” or “regulation” refers to a decrease in weight.

For example, the polypeptide or polynucleotide or host cell as described herein maintains the weight of a subject or increases the weight of a subject.

Without wishing to be bound by theory, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein exerts a stimulatory effect on the appetite of a subject by downregulating the expression of genes associated with the suppression of appetite (such as genes encoding satiety hormones). Agt, Cartpt, Cck, Cxcl12 and Gcg are examples of genes associated with regulating appetite and the downregulation of one or more of these genes is associated with the suppression of appetite.

Cholecystokinin (Cck) and glucagon (Gcg) are examples of satiety hormones.

In one aspect, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein stimulates the appetite in the subject such that the subject consumes at least 5%, 10%, or 15% more food after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject. In addition, or alternatively, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein stimulates the appetite in the subject such that after 1 month from first administration of the polypeptide or polynucleotide or host cell as described herein the weight of the subject is at least 2%, 5%, or 10% higher when compared to the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding

HP or the host cell as described herein reduces the level of cholecystokinin (Cck) and/or glucagon (Gcg) in the blood of a subject.

In one aspect, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein reduces the level of cholecystokinin (Cck) and/or glucagon (Gcg) in the blood of a subject by at least 5%, 10%, 15% or 20% after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein downregulates the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject.

In one aspect, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein decreases the expression of the gene encoding cholecystokinin (Cck) such that the expression level (e.g. mRNA level) is at least 5%, 10%, 15% or 20% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the expression level in the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one aspect, the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein decreases the expression of the gene encoding glucagon (Gcg) such that the expression level (e.g. mRNA level) is at least 5%, 10%, 15% or 20% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the expression level in the subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Maintaining the Length of Part of the Intestine

In one embodiment polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to maintain the length of part of the intestine (such as the large intestine and/or small intestine) of a subject.

Examples of sections (i.e. parts) of the intestine include the small intestine (e.g. the duodenum, the jejunum and the ileum) and/or the large intestine (e.g. the caecum, ascending colon, transverse colon, descending colon, and sigmoid colon).

The term “maintains the length” as used herein refers to there being no or only a small change in the length of part of the intestine after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the length of that part of the intestine before administration of the polypeptide or polynucleotide or host cell as described herein.

In one embodiment, the polypeptide or polynucleotide sequence or host cell as described herein prevents a reduction in the length of large intestine. In addition or alternatively, the polypeptide or polynucleotide sequence or host cell as described herein prevents an increase in the length of the small intestine.

In one embodiment, a small change in the length of the large intestine of a subject is a reduction in length of less than 5%, 2% or 1% after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the length of the large intestine in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, a small change in the length of the small intestine of a subject is an increase in length of less than 1%, 2%, 5%, 7% or 10% after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the length of the small intestine in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Intestine Disruption

In one embodiment, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to reduce disruption to the intestine (e.g. large intestine) of a subject (such as a subject with IBD).

The term “disruption to the intestine of a subject” as used herein refers to an affect on the integrity of the mucosal epithelium and/or an affect on the number of goblet cells in the epithelium and/or an affect on the number of immune cells infiltrating the lamina propria.

In one embodiment, the polypeptide or polynucleotide sequence or host cell of the description reduces or prevents disruption to the integrity of the mucosal epithelium and/or reduces or prevents a reduction in the number of goblet cells in the epithelium and/or reduces or prevents the infiltration of immune cells into the lamina propria.

In one embodiment, a reduction in disruption to the integrity of the mucosal epithelium is a reduction of at least 5%, 10%, 15% or 20% in the numbers of bacteria crossing from the intestinal lumen into intestinal cells after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of bacteria crossing from the intestinal lumen into intestinal cells in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, an increase in the number of goblet cells in the epithelium is an increase of at least 2%, 5%, 10%, 15% or 20% in the numbers of goblet cells in the epithelium of a subject after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the number goblet cells in the epithelium of a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

In one embodiment, the reduction in the infiltration of immune cells into the lamina propria is such that over a fixed time period (such as 24 hours) there is a reduction of at least 5%, 10%, 15%, 20% or 30% in the numbers of immune cells (e.g. T cells) crossing into lamina propria after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the numbers of immune cells (e.g. T cells) crossing from the into lamina propria cells in a subject before the polypeptide HP or the polynucleotide sequence encoding HP or the host cell as described herein is administered to the subject.

Pro-Inflammatory Genes and Barrier Integrity Genes

In one embodiment, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to regulate the expression of one or more pro-inflammatory genes and/or anti-inflammatory genes and/or one or more barrier integrity genes in a cell or cells of a subject.

In one embodiment, the term “regulate” refers to an upregulation in the expression of one or more pro-inflammatory genes or anti-inflammatory genes. In an alternative embodiment, the term “regulate” refers to a downregulation in the expression of one or more pro-inflammatory genes or anti-inflammatory genes.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein downregulates the expression of one or more pro-inflammatory genes in a cell or cells of a subject.

The term “pro-inflammatory gene” as used herein refers to a gene which, when expressed, promotes inflammation. Examples of pro-inflammatory genes include genes encoding but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ, CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α.

In one embodiment, the pro-inflammatory gene is selected from the group consisting of IL6, CXCL10, and TNF-α.

In one embodiment, the expression level (e.g. mRNA level) of one or more pro-inflammatory genes is decreased (i.e. downregulated) such that the level is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

The term “barrier integrity genes” as used herein refers to a gene which, when expressed, has a role in the function of the barrier of the intestine such as the repair of the barrier and the prevention of microorganisms crossing the barrier. Examples of barrier integrity genes include genes encoding RetnIg|Retnlb, Si, Defa24, Hsd11b2, Hsd17b2, and Nr1d1|Thra.

In one embodiment, the term “regulate” refers to an upregulation in the expression of one or more barrier integrity genes. In an alternative embodiment, the term “regulate” refers to a downregulation in the expression of one or more barrier integrity genes.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein upregulates the expression of barrier integrity genes in a cell or cells of a subject

In one embodiment, the barrier integrity gene is selected from the group consisting of RetnIg|Retnlb, Si, Defa24, Hsd11b2, Hsd17b2, and Nr1d1|Thra.

In one embodiment, the expression level (e.g. mRNA level) of one or more barrier integrity genes is increased (i.e. upregulated) such that the level is at least 10%, 20%, 30%, 40% or 50% higher after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

In one embodiment, the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein upregulates the expression of anti-inflammatory genes.

Regulating Gene Expression

In one embodiment, the polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used in regulating the expression in a cell or cells of a subject (such as a subject with IBD) of one or more genes selected from the group consisting of regenerating islet-derived 3 beta gene (Reg3b), resistin-like gamma resistin like beta gene (RetnIg|Retnlb), sucrase-isomaltase (alpha-glucosidase) gene (Si), defensin alpha 24 gene (Defa24), hydroxysteroid 11-beta dehydrogenase 2 gene (Hsd11b2), hydroxysteroid (17-beta) dehydrogenase 2 gene (Hsd17b2), resistin-Like Molecule-beta (RELMb), and nuclear receptor 1D1 thyroid hormone receptor alpha gene (Nr1d1|Thra).

The terms “Reg”, “Reg3” and “Reg3b” as used herein are interchangeable.

The terms “Hsd”, “Hsd17b2” or “Hsd17b2” as used herein are interchangeable.

In one embodiment, the term “regulate” refers to an upregulation in the expression of the genes. In an alternative embodiment, the term “regulate” refers to a downregulation in the expression of the genes.

The present invention is useful in regulating the expression of pro-inflammatory genes and/or barrier integrity genes.

For the avoidance of doubt, pro-inflammatory genes include IL-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNα, CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13 and TNF-α.

For the avoidance of doubt, barrier integrity genes include RetnIg/Retnlb, Si, Defa24, Hsd11b2, Hsd17b2, and Nrd1\Thra.

In one embodiment, the polypeptide or polynucleotide sequence or host cell as described herein decreases the expression of one or more genes selected from the group consisting of regenerating islet-derived 3 beta gene (Reg3b); resistin-like gamma resistin like beta gene (RetnIg|Retnlb); resistin-Like Molecule-beta (RELMb), sucrase-isomaltase (alpha-glucosidase) gene (Si); and defensin alpha 24 gene (Defa24). For example, the expression level (e.g. mRNA level) of one or more genes selected from the group is decreased (i.e. downregulated) such that the level is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

In one embodiment, the polypeptide or polynucleotide sequence or host cell as described herein increases the expression of one or more genes selected from the group consisting of hydroxysteroid 11-beta dehydrogenase 2 gene (Hsd11b2); hydroxysteroid (17-beta) dehydrogenase 2 gene (Hsd17b2); and nuclear receptor 1D1 thyroid hormone receptor alpha gene (Nr1d1|Thra). For example, the expression level (e.g. mRNA level) of one or more genes selected from the group is increased (i.e. upregulated) such that the level is at least 10%, 20%, 30%, 40% or 50% higher after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

Proinflammatory Pathways

In one embodiment, polypeptide HP or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to reduce the activation of pro-inflammatory pathways in a cell or cells of a subject.

The reduction in the activation of pro-inflammatory pathways can be determined by determining the inflammation in a subject.

Inflammation in a subject can be determined by determining the levels of pro-inflammatory cytokines and chemokines in tissue, serum and/or faecal samples in a subject before, and after, the polypeptide or polynucleotide or host cell as described herein is administered to the subject. For example, the levels of one or more of the following can be monitored: IL-1, IL-4, IL5, IL6, IL-8, IL-12, IL-13, IL-17, IL-21, IL-22, IL23, TNFα, IFNγ, CXCL1, CXCL10, CCL20 serum and faecal calprotectin, SA1009/SA1008 calcium binding proteins, and Type 1 interferons, CD markers such as CD163, CD14, inflammatory transcription factors such as NF-κβ, STAT, and MAPkinases, c-reactive protein (CRP), erythrocyte sedimentation rate (ESR), complement proteins, serum albumin, histological evaluation of target tissues and organs, disease activity indices.

In one embodiment, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used to reduce the activity and/or expression of NF-κβ in a cell or cells (such as epithelial cells, epidermal cells, neuronal cells, liver, spleen, kidney, lung, heart and/or pancreatic cells) of a subject.

For example, the activity of NF-κβ is decreased such that the activity of NF-κβ is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

For example, the expression level (e.g. mRNA) of NF-κβ is decreased (i.e. downregulated) such that the level is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or the host cell as described herein is administered to the subject.

Alimentary Canal

Parts of the alimentary canal include the mouth, the oesophagus, the stomach and the intestine (such as the small intestine (e.g. the duodenum, the jejunum and the ileum) and/or the large intestine (e.g. the caecum, ascending colon, transverse colon, descending colon, and sigmoid colon).

Herein, the term “large intestine” may be used interchangeably with the term “colon”.

In one embodiment, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used for improving alimentary canal health in a subject.

The term “improving alimentary canal health” as used herein refers to reducing the level of inflammation in the alimentary canal or part thereof and/or improving intestinal microbiota.

In one embodiment, the level of inflammation in the alimentary canal is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level of inflammation in the alimentary canal of a subject before the polypeptide or polynucleotide or host cell as described herein is administered to the subject.

In one embodiment, polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, is used for improving intestinal microbiota in a subject.

The term “intestinal microbiota” as used herein refers to microorganisms that live in the digestive tract of the host animals. These microorganisms perform a wide variety of metabolic, structural, protective and other beneficiary functions.

As used herein, the term “improving intestinal microbiota” refers to increasing the number and/or type of desirable microorganisms present in the intestine of a subject (e.g. the host), and/or increasing the activity of said desirable microorganisms in terms of their metabolic, structural, protective and other beneficiary functions. The term “improving intestinal microbiota” may also refer to decreasing the number and/or type of undesirable microorganisms present in the intestine of a subject (e.g. the host), and/or decreasing the activity of said undesirable microorganisms in terms of their metabolic, structural, protective and other beneficiary functions.

Microorganisms which are desirable in the intestine of a host are those microorganisms which have a protective and beneficiary function. Firmicutes and/or Bacteroidetes bacteria are examples of desirable microorganisms in the intestine of a host.

Microorganisms which are undesirable in the intestine of a host are those microorganisms which can interfere with the metabolic, structural, protective and other beneficiary functions of desirable microorganisms in the intestine have a protective and beneficiary function. In addition or alternatively, undesirable microorganisms are those which cause, for example, inflammation and/or diarrhoea. E. coli (ETEC, EPEC, EIEC, EHEC and/or EAEC) is an example of an undesirable microorganism in the intestine of a host.

For example, the numbers (i.e. levels) of Firmicutes and/or Bacteroidetes bacteria are increased and the numbers of E. coli are reduced; such an improvement in intestinal microbiota may occur in subjects with inflammatory bowel disease (IBD) once the polypeptide HP or the polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence has been administered to the subject.

In one embodiment, the number of desirable microorganisms (such as Firmicutes and/or Bacteroidetes bacteria) present in the intestine of a subject (e.g. the host), is increased such that the number of microorganisms is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before the polypeptide or polynucleotide or host cell as described herein is administered to the subject. In addition, or alternatively, the types of desirable microorganisms (such as Clostridium cluster XIVa bacteria) present in the intestine of a subject (e.g. the host), are increased such that there are at least 2%, 5%, 10%, or 15% more types of microorganisms after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the types in the subject before the polypeptide or polynucleotide or host cell as described herein is administered to the subject.

In one embodiment, the protein of the invention modifies the bacterial composition in the intestine of a subject to provide a beneficial microbiota. For example, the number of undesirable microorganisms (such as E. coli (ETEC, EPEC, EIEC, EHEC and/or EAEC)) present in the intestine of a subject (e.g. the host), is decreased such that the number of microorganisms is at least 10%, 20%, 30%, 40% or 50% lower after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the level in the subject before the polypeptide or polynucleotide or host cell as described herein is administered to the subject. In addition, or alternatively, the types of undesirable microorganisms (such as E. coli) present in the intestine of a subject (e.g. the host), are decreased such that there are at least 1%, 2%, 5%, or 10%, fewer types of undesirable microorganisms after administration of the polypeptide or polynucleotide or host cell as described herein when compared to the types in the subject before the polypeptide or polynucleotide or host cell as described herein is administered to the subject.

Encapsulation

In one embodiment, the polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence is encapsulated.

In a further embodiment, a pharmaceutical composition comprising the polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence is encapsulated.

In another embodiment, a nutritional supplement comprising the polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence encoding said polypeptide is encapsulated.

In a further embodiment, a feedstuff, food product, dietary supplement, or food additive as described herein is encapsulated.

The term “encapsulated” as used herein refers to a means for protecting the polypeptide or polynucleotide or host cell as described herein from an incompatible environment by physical separation so that it can be delivered to the target site (e.g. the intestine) without degradation or significant degradation in order that the polypeptide or polynucleotide or host cell can have an effect on the target site. An example is an enteric coated capsule or an enterically-resistant capsule.

Even when the objective of the encapsulation is the isolation of the polypeptide or polynucleotide or host cell from its surroundings, the protective coating or shell must be ruptured at the time of desired action. The rupturing of the protective coating or shell is typically brought about through the application of chemical and physical stimuli such as pressure, enzyme attack, chemical reaction and physical disintegration.

For example, encapsulation ensures that the polypeptide or polynucleotide or host cell can be ingested so that the polypeptide or polynucleotide or host cell can be delivered to the target site (e.g. the intestine) in an amount which is effective to produce an effect at the target site.

Pharmaceutical Composition

In one embodiment, a pharmaceutical composition comprises polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, and optionally a pharmaceutically acceptable excipient, carrier or diluent.

The pharmaceutical composition may be any pharmaceutical composition. In one aspect, the pharmaceutical composition is to be administered orally, enterally or rectally. For example, the composition may be an edible composition. “Edible” means a material that is approved for human or animal consumption.

The pharmaceutical compositions may be for human or animal usage in human and veterinary medicine.

Examples of such suitable excipients for the various different forms of pharmaceutical compositions described herein may be found in the “Handbook of Pharmaceutical Excipients, 2nd Edition, (1994), Edited by A Wade and P J Weller.

Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985).

Examples of suitable carriers include lactose, starch, glucose, methyl cellulose, magnesium stearate, mannitol, sorbitol and the like.

Examples of suitable diluents include one or more of: water, ethanol, glycerol, propylene glycol and glycerin, and combinations thereof.

The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may comprise as, or in addition to, the carrier, excipient or diluent any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s).

Examples of suitable binders include starch, gelatin, natural sugars such as glucose, anhydrous lactose, free-flow lactose, beta-lactose, corn sweeteners, natural and synthetic gums, such as acacia, tragacanth or sodium alginate, carboxymethyl cellulose and polyethylene glycol.

Examples of suitable lubricants include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and the like.

Preservatives, stabilizers, dyes and even flavouring agents may be provided in the pharmaceutical composition. Examples of preservatives include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. Antioxidants and suspending agents may be also used.

In one aspect, the polypeptide or polynucleotide sequence or host cell of the pharmaceutical composition is encapsulated.

In another aspect, the polypeptide of the pharmaceutical composition is a recombinant polypeptide.

In a further aspect, the polynucleotide sequence of the pharmaceutical composition encodes a recombinant polypeptide.

In another aspect, the host cell of the pharmaceutical composition produces or is capable of producing a recombinant polypeptide.

In a further aspect, an expression vector comprises said polynucleotide sequence of the pharmaceutical composition.

The pharmaceutical may be in the form of a solution or as a solid—depending on the use and/or the mode of application and/or the mode of administration.

As used herein, the term “medicament” encompasses medicaments for both human and animal usage in human and veterinary medicine. In addition, the term “medicament” as used herein means any substance, which provides a therapeutic and/or beneficial effect. The term “medicament” as used herein is not necessarily limited to substances, which need Marketing Approval, but may include substances which, can be used in cosmetics, nutraceuticals, food (including feeds and beverages for example), probiotic cultures, nutritional supplements and natural remedies. In addition, the term “medicament” as used herein encompasses a product designed for incorporation in animal feed, for example livestock feed and/or pet food.

Nutritional Supplements

Nutritionally acceptable carriers, diluents and excipients include those suitable for human or animal consumption and that are used as standard in the food industry. Typical nutritionally acceptable carriers, diluents and excipients will be familiar to the skilled person in the art.

In one embodiment, a nutritional supplement comprises polypeptide HP, or a polynucleotide sequence encoding polypeptide HP, or a host cell comprising said polynucleotide sequence, or a host cell comprising an expression vector comprising said polynucleotide sequence, and a nutritional acceptable excipient, carrier or diluent.

In one example, the polypeptide or polynucleotide sequence or host cell of the nutritional supplement is encapsulated.

In another example, the polypeptide of the nutritional supplement is a recombinant polypeptide.

In a further aspect, the polynucleotide sequence of the nutritional supplement encodes a recombinant polypeptide.

In another aspect, the host cell of the nutritional supplement produces or is capable of producing a recombinant polypeptide.

In a further example, the polynucleotide of the nutritional supplement is comprised in an expression vector.

Feedstuff/Products

A further aspect of the invention relates to feedstuffs, food products, dietary supplements and food additives comprising polypeptide HP or a polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence.

The terms “feedstuff”, “food product” “food additive” and “dietary supplement” as used herein are intended to cover all consumable products that can be solid, jellied or liquid.

The term “food product” is used in a broad sense—and covers food for humans as well as food for animals (i.e. a feed). In one aspect, the food product is for human consumption. Examples of food products include diary products (such as milk, cheese, beverages comprising whey protein, milk drinks, lactic acid bacteria drinks, yoghurt, drinking yoghurt), bakery products, beverages and beverage powders.

The “feedstuff”, “food product” “food additive” and “dietary supplement” may be in the form of a solution or as a solid—depending on the use and/or the mode of application and/or the mode of administration.

As used herein the term “dietary supplement” includes a formulation which is or can be added to a food product or feedstuff as a nutritional supplement. The term “dietary supplement” as used here also refers to formulations which can be used at low levels in a wide variety of products that require gelling, texturising, stabilising, suspending, film-forming and structuring, retention of juiciness and improved mouthfeel, without adding viscosity.

Suitable food products may include, for example, functional food products, food compositions, pet food, livestock feed, health foods, feedstuffs and the like. In one aspect, the food product is a health food.

As used herein, the term “functional food product” means food that is capable of providing not only a nutritional effect, but is also capable of delivering a further beneficial effect to the consumer. Accordingly, functional foods are ordinary foods that have components or ingredients (such as those described herein) incorporated into them that impart to the food a specific functional—e.g. medical or physiological benefit—other than a purely nutritional effect.

Examples of specific food products that are applicable to the present invention include milk-based products, ready to eat desserts, powders for re-constitution with, e.g., milk or water, chocolate milk drinks, malt drinks, ready-to-eat dishes, instant dishes or drinks for humans or food compositions representing a complete or a partial diet intended for pets or livestock.

In one aspect, the feedstuff, food product, dietary supplement or food additive according to the present invention are intended for humans, pets or livestock such as monogastric animals. The feedstuff, food product, dietary supplement or food additive may be intended for animals selected from the group consisting of dogs, cats, pigs, horses, or poultry. In a further embodiment, the food product, dietary supplement or food additive is intended for adult species, in particular human adults.

The term “milk-based product” as used herein means any liquid or semi-solid milk or whey based product having a varying fat content. The milk-based product can be, e.g., cow's milk, goat's milk, sheep's milk, skimmed milk, whole milk, milk recombined from powdered milk and whey without any processing, or a processed product, such as yoghurt, curdled milk, curd, sour milk, sour whole milk, butter milk and other sour milk products. Another important group includes milk beverages, such as whey beverages, fermented milks, condensed milks, infant or baby milks; flavoured milks, ice cream; milk-containing food such as sweets.

The feedstuffs, food products, dietary supplements or food additives of the present invention may be—or may be added to—food supplements, also referred to herein as dietary or nutritional supplements or food additives.

The feedstuffs, food products, dietary supplements or food additives according to the invention may also be used in animal nutrition (e.g. in pig nutrition), particularly in the early-weaned period and growing fattening period. The feedstuffs, food products, dietary supplements or food additives are expected to enhance immune function reduce and prevent infectious diseases, beneficially alter the microbiota composition, and improve growth and performance of animals, for example, through increased feed conversion efficiency.

In one embodiment the feedstuff, food product, dietary supplement, or food additive is encapsulated.

In one embodiment, the polypeptide of the feedstuff, food product, dietary supplement, or food additive is a recombinant polypeptide.

In one example, the polynucleotide of the feedstuff, food product, dietary supplement, or food additive is comprised in an expression vector.

Administration

The pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention may be adapted for oral, rectal, vaginal, parenteral, intramuscular, intraperitoneal, intraarterial, intrathecal, intrabronchial, subcutaneous, intradermal, intravenous, nasal, buccal or sublingual routes of administration.

In one aspect, the pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention are adapted for oral, rectal, vaginal, parenteral, nasal, buccal or sublingual routes of administration.

In a further aspect, the pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention are adapted for oral administration.

For oral administration, particular use is made of compressed tablets, pills, tablets, gellules, drops, and capsules.

Other forms of administration comprise solutions or emulsions which may be injected intravenously, intraarterially, intrathecally, subcutaneously, intradermally, intraperitoneally or intramuscularly, and which are prepared from sterile or sterilisable solutions. The pharmaceutical compositions of the present invention may also be in form of suppositories, pessaries, suspensions, emulsions, lotions, ointments, creams, gels, sprays, solutions or dusting powders.

An alternative means of transdermal administration is by use of a skin patch. For example, the active ingredient can be incorporated into a cream consisting of an aqueous emulsion of polyethylene glycols or liquid paraffin. In another example, the active ingredient can also be incorporated into an ointment consisting of a white wax or white soft paraffin base together with such stabilisers and preservatives as may be required.

Pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives may be formulated in unit dosage form, i.e., in the form of discrete portions containing a unit dose, or a multiple or sub-unit of a unit dose.

Dosage

A person of ordinary skill in the art can easily determine an appropriate dose of polypeptide HP or a polynucleotide sequence or a host cell as described herein to administer to a subject without undue experimentation. Typically, a physician will determine the actual dosage which will be most suitable for an individual patient and it will depend on a variety of factors including the activity of the specific bacterial strain employed, the metabolic stability and length of action of that strain, the age, body weight, general health, sex, diet, mode and time of administration, rate of excretion, drug combination, the severity of the particular condition, and the individual undergoing therapy. The dosages disclosed herein are exemplary of the average case. There can of course be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention.

Combinations

In one aspect, polypeptide HP or a polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence are administered in combination with one or more other active agents. In such cases, polypeptide HP or a polynucleotide sequence encoding polypeptide HP or a host cell comprising said polynucleotide sequence or a host cell comprising an expression vector comprising said polynucleotide sequence may be administered consecutively, simultaneously or sequentially with the one or more other active agents.

For instance, at least two of the polypeptide HP, the polynucleotide sequence and the host cell as described herein are administered to the subject.

For example, one type of host cell according the present invention (e.g. a L. lactis transformed with a polynucleotide sequence encoding HP) may be combined with another type of host cell according to the present invention (e.g. a Lactobacillus spp transformed with a polynucleotide sequence encoding HP).

In another example, one type of host cell according the present invention (e.g. a L. lactis transformed with a polynucleotide sequence encoding HP) may be combined with another microorganism such as Bacteroides spp (such as Bacteroides thetaiotaomicron), Lactococcus spp (such as L. lactis), Lactobacillus spp, Bifidobacterium spp, and Streptococcus spp (such as Streptococcus thermophilus).

Polynucleotide Sequence

The scope of the present description encompasses polynucleotide sequences encoding HP polypeptides.

The term “nucleotide sequence” as used herein refers to an oligonucleotide sequence or polynucleotide sequence, and variant, homologues, fragments and derivatives thereof (such as portions thereof). The nucleotide sequence may be of genomic or synthetic or recombinant origin, which may be double-stranded or single-stranded whether representing the sense or anti-sense strand.

The term “nucleotide sequence” in relation to the present description includes genomic DNA, cDNA, synthetic DNA, and RNA. In one embodiment it means cDNA sequence.

In one embodiment, the nucleotide sequence when relating to and when encompassed by the per se scope of the present description does not include the native nucleotide sequence when in its natural environment and when it is linked to its naturally associated sequence(s) that is/are also in its/their natural environment. For ease of reference, herein this embodiment is called the “non-native nucleotide sequence”. In this regard, the term “native nucleotide sequence” means an entire nucleotide sequence that is in its native environment and when operatively linked to an entire promoter with which it is naturally associated, which promoter is also in its native environment. However, the amino acid sequence encompassed by scope the present description can be isolated and/or purified post expression of a nucleotide sequence in its native organism. In one embodiment, however, the amino acid sequence encompassed by scope of the present description may be expressed by a nucleotide sequence in its native organism but wherein the nucleotide sequence is not under the control of the promoter with which it is naturally associated within that organism.

Typically, the nucleotide sequence encompassed by the scope of the present description is prepared using recombinant DNA techniques (i.e. recombinant DNA). However, in an alternative embodiment of the invention, the nucleotide sequence could be synthesised, in whole or in part, using chemical methods well known in the art (see Caruthers M H et al., (1980) Nuc Acids Res Symp Ser 215-23 and Horn T et al., (1980) Nuc Acids Res Symp Ser 225-232).

The polynucleotide encompassed in the present description may be used in conjunction with other polynucleotide sequences. Thus the present description also covers a combination of polynucleotide sequences wherein the combination comprises the polynucleotide sequence encoding HP and another polynucleotide sequence, which may be another polynucleotide sequence encoding HP.

Preparation of the Nucleotide Sequence

A nucleotide sequence encoding either a peptide of the present description may be identified and/or isolated and/or purified from any cell or organism producing said peptide. Various methods are well known within the art for the identification and/or isolation and/or purification of nucleotide sequences. By way of example, DNA amplification techniques to prepare more of a sequence may be used once a suitable sequence has been identified and/or isolated and/or purified.

By way of further example, a genomic DNA and/or cDNA library may be constructed using chromosomal DNA or messenger RNA from the organism producing the peptide. If the amino acid sequence is known, labelled oligonucleotide probes may be synthesised and used to identify clones from the genomic library prepared from the organism. Alternatively, a labelled oligonucleotide probe containing sequences homologous to a similar known gene could be used to identify clones. In the latter case, hybridisation and washing conditions of lower stringency are used.

Alternatively, clones comprising the peptides of the present description could be identified by inserting fragments of genomic DNA into an expression vector, such as a plasmid, transforming bacteria with the resulting genomic DNA library, and then plating the transformed bacteria onto agar plates containing a substrate for the peptide thereby allowing clones expressing the peptide to be identified.

In a yet further alternative, the nucleotide sequence encoding the peptide may be prepared synthetically by established standard methods, e.g. the phosphoroamidite method described by Beucage S. L. et al., (1981) Tetrahedron Letters 22, p 1859-1869, or the method described by Matthes et al., (1984) EMBO J. 3, p 801-805. In the phosphoroamidite method, oligonucleotides are synthesised, e.g. in an automatic DNA synthesiser, purified, annealed, ligated and cloned in appropriate vectors.

The nucleotide sequence may be of mixed genomic and synthetic origin, mixed synthetic and cDNA origin, or mixed genomic and cDNA origin, prepared by ligating fragments of synthetic, genomic or cDNA origin (as appropriate) in accordance with standard techniques. Each ligated fragment corresponds to various parts of the entire nucleotide sequence. The DNA sequence may also be prepared by polymerase chain reaction (PCR) using specific primers, for instance as described in U.S. Pat. No. 4,683,202 or in Saiki R K et al., (Science (1988) 239, pp 487-491).

Amino Acid Sequences

The scope of the present description also encompasses HP polypeptides as defined herein.

The amino acid sequence may be prepared/isolated from a suitable source, or it may be made synthetically or it may be prepared by use of recombinant DNA techniques.

The polypeptide encompassed in the present description may be used in conjunction with other peptides. Thus the present description also covers a combination of peptides wherein the combination comprises the polypeptide HP and another peptide, which may be another HP polypeptide.

The amino acid sequence when relating to and when encompassed by the per se scope of the present invention is not a native peptide. In this regard, the term “native peptide” means an entire peptide that is in its native environment and when it has been expressed by its native nucleotide sequence.

Recombinant Polypeptide

In one aspect the polypeptide sequence for use in the present invention is a recombinant sequence—i.e. a sequence that has been prepared using recombinant DNA techniques (such as the expression of the polypeptide using a host cell comprising an expression vector encoding the polypeptide).

These recombinant DNA techniques are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press.

Fusion Proteins

The polypeptide sequence for use according to the present invention may be produced as a fusion protein, for example to aid in extraction and purification. Examples of fusion protein partners include glutathione-S-transferase (GST), 6×His, GAL4 (DNA binding and/or transcriptional activation domains) and (β-galactosidase). It may also be convenient to include a proteolytic cleavage site between the fusion protein partner and the protein sequence of interest to allow removal of fusion protein sequences.

Typically, the fusion protein will not hinder the activity of the protein sequence.

Gene fusion expression systems in E. coli have been reviewed in Curr Opin Biotechnol (1995) 6(5):501-6.

In another embodiment of the description, the polypeptide sequence may be ligated to a heterologous sequence to encode a fusion protein. For example, for screening of peptide libraries for agents capable of affecting the substance activity, it may be useful to encode a chimeric substance expressing a heterologous epitope that is recognised by a commercially available antibody.

Sequence Identity or Sequence Homology

The terms “polypeptide”, “polypeptide sequence”, “peptide”, “protein” and “amino acid sequence” are used interchangeably herein.

The terms “polynucleotide sequence” and “nucleotide sequence” are used interchangeably herein.

The present invention also encompasses the use of sequences having a degree of sequence identity or sequence homology with amino acid sequence(s) of a polypeptide described herein (e.g. variants, homologues and derivatives) or of any nucleotide sequence encoding such a polypeptide (hereinafter referred to as a “homologous sequence(s)”). Here, the term “homologue” means an entity having a certain homology with the subject amino acid sequences and the subject nucleotide sequences. Here, the term “homology” can be equated with “identity”.

In the present context, a homologous sequence is taken to include an amino acid or a nucleotide sequence which may be at least 50, 60, 70, 75, 80, 85 or 90% identical, in some embodiments at least 95, 96, 97, 98 or 99% identical to the subject sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity.

In some embodiments, a homologous sequence is taken to include an amino acid sequence or nucleotide sequence which has one or several additions, deletions and/or substitutions compared with the subject sequence.

In some embodiments, the present invention relates to the use of a protein whose amino acid sequence is represented herein or a protein derived from this (parent) protein by substitution, deletion or addition of one or several amino acids, such as 2, 3, 4, 5, 6, 7, 8, 9 amino acids, or more amino acids, such as 10 or more than 10 amino acids in the amino acid sequence of the parent protein and having the activity of the parent protein.

In some embodiments, the present invention relates to the use of a nucleic acid sequence (or gene) encoding a protein whose amino acid sequence is represented herein or encoding a protein derived from this (parent) protein by substitution, deletion or addition of one or several amino acids, such as 2, 3, 4, 5, 6, 7, 8, 9 amino acids, or more amino acids, such as 10 or more than 10 amino acids in the amino acid sequence of the parent protein and having the activity of the parent protein.

In the present context, a homologous sequence is taken to include a nucleotide sequence which may be at least 50, 60, 70, 75, 85 or 90% identical, in some embodiments at least 95, 96, 97, 98 or 99% identical to a nucleotide sequence encoding a polypeptide described herein (the subject sequence). Typically, the homologues will comprise the same or equivalent sequences that code for the domain(s) etc. as the subject sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity.

The homologous amino acid sequence and/or nucleotide sequence may provide and/or encode a polypeptide which retains the functional activity and/or enhances the activity of the polypeptide.

In some aspects, an amino acid sequence as described herein has at least 50, 60, 70, 75, 80, 85 or 90% identity, in some embodiments at least 95, 96, 97, 98 or 99% identity to the subject sequence.

In some aspects, a nucleotide sequence as described herein has at least 50, 60, 70, 75, 80, 85 or 90% identity, in some embodiments at least 95, 96, 97, 98 or 99% identity to the subject sequence.

Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % homology between two or more sequences.

homology may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid in one sequence is directly compared with the corresponding amino acid in the other sequence, one residue at a time. This is called an “ungapped” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.

Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an otherwise identical pair of sequences, one insertion or deletion will cause the following amino acid residues to be put out of alignment, thus potentially resulting in a large reduction in % homology when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without penalizing unduly the overall homology score. This is achieved by inserting “gaps” in the sequence alignment to try to maximize local homology.

However, these more complex methods assign “gap penalties” to each gap that occurs in the alignment so that, for the same number of identical amino acids, a sequence alignment with as few gaps as possible—reflecting higher relatedness between the two compared sequences—will achieve a higher score than one with many gaps. “Affine gap costs” are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties will of course produce optimized alignments with fewer gaps. Most alignment programs allow the gap penalties to be modified. Typically the default values are used when using such software for sequence comparisons.

Calculation of maximum % homology therefore firstly requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for carrying out such an alignment is the Vector NTI (Invitrogen Corp.). Examples of software that can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al 1999 Short Protocols in Molecular Biology, 4th Ed—Chapter 18), BLAST 2 (see FEMS Microbiol Lett 1999 174(2): 247-50; FEMS Microbiol Lett 1999 177(1): 187-8 and tatiana@ncbi.nlm.nlh.gov), FASTA (Altschul et al 1990 J. Mol. Biol. 403-410) and AlignX for example. At least BLAST, BLAST 2 and FASTA are available for offline and online searching (see Ausubel et al 1999, pages 7-58 to 7-60).

Although the final % homology can be measured in terms of identity, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix—the default matrix for the BLAST suite of programs. Vector NTI programs generally use either the public default values or a custom symbol comparison table if supplied (see user manual for further details). For some applications, it is preferred to use the default values for the Vector NTI package.

Alternatively, percentage homologies may be calculated using the multiple alignment feature in Vector NTI (Invitrogen Corp.), based on an algorithm, analogous to CLUSTAL (Higgins DG & Sharp PM (1988), Gene 73(1), 237-244).

Once the software has produced an optimal alignment, it is possible to calculate homology, for example % sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result.

Should Gap Penalties be used when determining sequence identity, then the following parameters can be used for pairwise alignment for example:

FOR BLAST GAP OPEN 0 GAP EXTENSION 0 FOR CLUSTAL DNA PROTEIN WORD SIZE 2 1 K triple GAP PENALTY 15 10 GAP EXTENSION 6.66 0.1

In one embodiment, CLUSTAL may be used with the gap penalty and gap extension set as defined above.

In one embodiment, the degree of identity with regard to a nucleotide sequence is determined over at least 20 contiguous nucleotides, for example over at least 30 contiguous nucleotides, for example over at least 40 contiguous nucleotides, for example over at least 50 contiguous nucleotides, for example over at least 60 contiguous nucleotides, for example over at least 100 contiguous nucleotides, for example over at least 200 contiguous nucleotides, for example over at least 300 contiguous nucleotides.

In one embodiment, the degree of identity with regard to a nucleotide sequence may be determined over the whole sequence.

The sequences may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent substance. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the secondary binding activity of the substance is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine, valine, glycine, alanine, asparagine, glutamine, serine, threonine, phenylalanine, and tyrosine.

Conservative substitutions may be made, for example according to the Table below. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other:

ALIPHATIC Non-polar G A P I L V Polar - uncharged C S T M N Q Polar - charged D E K R AROMATIC H F W Y

The present invention also encompasses homologous substitution (substitution and replacement are both used herein to mean the interchange of an existing amino acid residue, with an alternative residue) that may occur i.e. like-for-like substitution such as basic for basic, acidic for acidic, polar for polar etc. Non-homologous substitution may also occur i.e. from one class of residue to another or alternatively involving the inclusion of unnatural amino acids such as ornithine (hereinafter referred to as Z), diaminobutyric acid ornithine (hereinafter referred to as B), norleucine ornithine (hereinafter referred to as O), pyriylalanine, thienylalanine, naphthylalanine and phenylglycine.

Replacements may also be made by unnatural amino acids include; alpha* and alpha-disubstituted* amino acids, N-alkyl amino acids*, lactic acid*, halide derivatives of natural amino acids such as trifluorotyrosine*, p-Cl-phenylalanine*, p-Br-phenylalanine*, p-I-phenylalanine*, L-allyl-glycine*, β-alanine*, L-α-amino butyric acid*, L-γ-amino butyric acid*, L-α-amino isobutyric acid*, L-ε-amino caproic acid^(#), 7-amino heptanoic acid*, L-methionine sulfone^(#)*, L-norleucine*, L-norvaline*, p-nitro-L-phenylalanine*, L-hydroxproline^(#), L-thioproline*, methyl derivatives of phenylalanine (Phe) such as 4-methyl-Phe*, pentamethyl-Phe*, L-Phe (4-amino)#, L-Tyr (methyl)*, L-Phe (4-isopropyl)*, L-Tic (1,2,3,4-tetrahydroisoquinoline-3-carboxyl acid)*, L-diaminopropionic acid # and L-Phe (4-benzyl)*. The notation * has been utilised for the purpose of the discussion above (relating to homologous or non-homologous substitution), to indicate the hydrophobic nature of the derivative whereas # has been utilised to indicate the hydrophilic nature of the derivative, #* indicates amphipathic characteristics.

Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or β-alanine residues. A further form of variation, involves the presence of one or more amino acid residues in peptoid form, will be well understood by those skilled in the art. For the avoidance of doubt, “the peptoid form” is used to refer to variant amino acid residues wherein the α-carbon substituent group is on the residue's nitrogen atom rather than the α-carbon. Processes for preparing peptides in the peptoid form are known in the art, for example Simon R J et al., PNAS (1992) 89(20), 9367-9371 and Horwell D C, Trends Biotechnol. (1995) 13(4), 132-134.

The nucleotide sequences for use in the present invention may include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones and/or the addition of acridine or polylysine chains at the 3′ and/or 5′ ends of the molecule. For the purposes of the present invention, it is to be understood that the nucleotide sequences described herein may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of nucleotide sequences of the present invention.

The present invention also encompasses the use of nucleotide sequences that are complementary to the sequences presented herein, or any derivative or fragment thereof. If the sequence is complementary to a fragment thereof then that sequence can be used as a probe to identify similar coding sequences in other organisms etc.

Polynucleotides which are not 100% homologous to the sequences of the present invention but fall within the scope of the invention can be obtained in a number of ways. Other variants of the sequences described herein may be obtained for example by probing DNA libraries made from a range of individuals, for example individuals from different populations. In addition, other homologues may be obtained and such homologues and fragments thereof in general will be capable of selectively hybridising to the sequences shown in the sequence listing herein. Such sequences may be obtained by probing cDNA libraries made from or genomic DNA libraries from other animal species, and probing such libraries with probes comprising all or part of any one of the sequences in the attached sequence listings under conditions of medium to high stringency. Similar considerations apply to obtaining species homologues and allelic variants of the polypeptide or nucleotide sequences of the invention.

Variants and strain/species homologues may also be obtained using degenerate PCR which will use primers designed to target sequences within the variants and homologues encoding conserved amino acid sequences within the sequences of the present invention. Conserved sequences can be predicted, for example, by aligning the amino acid sequences from several variants/homologues. Sequence alignments can be performed using computer software known in the art. For example the GCG Wisconsin PileUp program is widely used.

The primers used in degenerate PCR will contain one or more degenerate positions and will be used at stringency conditions lower than those used for cloning sequences with single sequence primers against known sequences.

Alternatively, such polynucleotides may be obtained by site directed mutagenesis of characterised sequences. This may be useful where for example silent codon sequence changes are required to optimise codon preferences for a particular host cell in which the polynucleotide sequences are being expressed. Other sequence changes may be desired in order to introduce restriction enzyme recognition sites, or to alter the property or function of the polypeptides encoded by the polynucleotides.

Polynucleotides (nucleotide sequences) of the invention may be used to produce a primer, e.g. a PCR primer, a primer for an alternative amplification reaction, a probe e.g. labelled with a revealing label by conventional means using radioactive or non-radioactive labels, or the polynucleotides may be cloned into vectors. Such primers, probes and other fragments will be at least 15, preferably at least 20, for example at least 25, 30 or 40 nucleotides in length, and are also encompassed by the term polynucleotides of the invention as used herein.

Polynucleotides such as DNA polynucleotides and probes according to the invention may be produced recombinantly, synthetically, or by any means available to those of skill in the art. They may also be cloned by standard techniques.

In general, primers will be produced by synthetic means, involving a stepwise manufacture of the desired nucleic acid sequence one nucleotide at a time. Techniques for accomplishing this using automated techniques are readily available in the art.

Longer polynucleotides will generally be produced using recombinant means, for example using a PCR (polymerase chain reaction) cloning techniques. The primers may be designed to contain suitable restriction enzyme recognition sites so that the amplified DNA can be cloned into a suitable cloning vector.

Recombinant Polynucleotide Sequence

In one aspect the polynucleotide sequence for use in the present invention is a recombinant polypeptide sequence—i.e. a sequence that has been prepared using recombinant DNA techniques (such as the expression of the polypeptide using a host cell comprising an expression vector encoding the polypeptide). Examples of recombinant polynucleotide sequences include codon optimised sequences and polynucleotide sequences encoding fusion polypeptide.

These recombinant DNA techniques are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press.

Synthetic

In one aspect the sequence for use in the present invention is a synthetic sequence—i.e. a sequence that has been prepared by in vitro chemical or enzymatic synthesis. It includes, but is not limited to, sequences made with optimal codon usage for host organisms—such as the methylotrophic yeasts Pichia and Hansenula.

The present invention is further described by way of the following non-limiting examples.

EXAMPLES

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA and immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press; Ausubel, F. M. et al. (1995 and periodic supplements; Current Protocols in Molecular Biology, ch. 9, 13, and 16, John Wiley & Sons, New York, N.Y.); B. Roe, J. Crabtree, and A. Kahn, 1996, DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; J. M. Polak and James O'D. McGee, 1990, In Situ Hybridization: Principles and Practice; Oxford University Press; M. J. Gait (Editor), 1984, Oligonucleotide Synthesis: A Practical Approach, Irl Press; D. M. J. Lilley and J. E. Dahlberg, 1992, Methods of Enzymology: DNA Structure Part A: Synthesis and Physical Analysis of DNA Methods in Enzymology, Academic Press; and E. M. Shevach and W. Strober, 1992 and periodic supplements, Current Protocols in Immunology, John Wiley & Sons, New York, N.Y. Each of these general texts is herein incorporated by reference.

Bacteroides thetaiotaomicron HP (BT0187, a pirin-related protein) was shown in an NF-κβ luciferase reporter assay, to greatly reduce NF-κβ activity stimulated in epithelial cells in culture by flagellin-, PMA- or IL-1.

For large scale production, HP (referred to as HP in FIGS. 1A and 1B with FIG. 1A showing the polynucleotide sequence and FIG. 1B showing the polypeptide sequence) was expressed in E. coli or L. lactis.

The sequence was codon optimised for expression in (i) E. coli (referred to as Rec 1 HP in FIG. 1B) and (ii) L. lactis (referred to as Rec 2 HP in FIG. 1B).

Isolated recombinant HP was tested in vitro and encapsulated.

The efficacy of the encapsulated product was evaluated in a rat model of inflammatory bowel disease (Dextran Sodium Sulphate [DSS]-induced colitis).

Example 1—the Effect of HP on Inflammatory Bowel Disease

Rat study: Hooded-Lister rats (Rowett strain; 6 month-old; —480 g) were reared, housed and managed under standard high quality conditions within the Bioresources of the Rowett Institute of Nutrition and Health. They had free access to sterile distilled water containing Dextran sodium sulphate (MP Biomedicals UK, Cambridge; DSS; 36000-50000 mol. wt.) for 7 days [days 1-5, 40g DSS/I and days 6-7, 20 g DSS/I]. Half of the DSS-treated rats were dosed daily (day 1-7) with HP protein and the remaining six DSS-treated rats were dosed daily (day 1-7) with placebo. Untreated controls had free access to sterile distilled water but were not dosed. Untreated controls had access to sterile distilled water. All rats had free access to high quality rodent chow. Food intake, water intake and body weight were measured daily.

The rats were euthanased (isoflurane overdose and exsanguination) and dissected on day 8. The total length of the colon was measured and a piece of ascending colon 3-6 cm from the caecal/colon junction was collected in OCT or fixed in neutral buffered formalin, 2-3 cm from the caecal/colon junction was placed in RNAlater and a piece 0-2 cm from the caecal/colon junction was snap frozen. A piece of descending colon 3-6 cm from the rectum was collected in OCT or fixed in neutral buffered formalin, 2-3 cm from the rectum was placed in RNAlater and a piece 0-2 cm from the rectum was snap frozen. The small intestine was measured, a piece of ileal tissue 5-7 cm from the ileocaecal junction was collected in OCT or fixed in neutral buffered formalin, 7-9 cm from the ileocaecal junction was collected for microbiology, 9-1 0 cm from the ileocaecal junction was placed in RNAlater and a piece 9-17 cm from the ileocaecal junction was snap frozen. Transverse colon was collected for microbiology as were mesenteric lymph nodes, liver and spleen. Lactose-fermenting and non-lactose fermenting bacteria in tissues were evaluated using MacConkey no 3 agar.

Fixed colon samples were embedded in 8100 Technovit resin. 4 μm sections were cut and stained with hematoxylin and eosin. Whole transverse cross-sectional areas were imaged and digitised using a Zeiss Axioskop microscope connected to a QImaging camera controlled by ImageProPlus software. These were examined in a blinded manner by 2 independent individuals and the severity of intestinal damage was graded based on the method of Berg et al. (1996) and data expressed as percentage of fields of view with pathology of 0 [no pathology] through to grade 3 [major pathology].

The rats treated with Dextran Sodium Sulphate (DSS) and rats treated with both DSS and HP (DSS/HP) had comparable water intake and so, the intake of DSS was also same between the treatment groups. At the same time, it was observed that the food intake by DSS rats was at a slightly lower rate than that of DSS/HP treated rats and controls. The DSS treated rats also tended to lose weight, while at the same time, the DSS/HP and control rats maintained their weight (FIGS. 2A-2C).

Rat colon length was reduced due to intake of DSS, a reported feature of DSS colitis. However, this change in the colon was prevented when rats were also treated with HP (FIG. 3). In contrast, small intestine length was increased with intake of DSS but unaltered in rats given DSS/HP (FIG. 3).

Mesenteric lymph nodes, liver and spleen of rats given DSS were sub-clinically infected with lactose (predominantly E. coli)-fermenting and non-lactose-fermenting bacteria (FIG. 4). This was not evident with DSS/HP. Spread of bacteria to these systemic tissues is likely to be result of loss of gut barrier integrity due to damage caused by DSS. HP appeared to prevent this loss of gut barrier integrity.

Histological analysis of ascending and descending colon was carried out (FIGS. 5A-5B & 6). The severity of intestinal damage was graded based on the method of Berg et al. (1996) and data expressed as percentage of fields of view with pathology of 0 [no pathology] through to grade 3 [major pathology] or as mean histopathology score. Disruption to the tissue caused by DSS was moderate and patchy, with varying degrees of damage (from little or none to severe) localised throughout the tissue sections. Overall, the integrity of the mucosal epithelium was impaired, there was a reduced number of goblet cells in the epithelium and infiltration of immune cells into the lamina propria. In contrast, overall disruption to the colon caused by DSS was greatly reduced by co-treatment of rats with HP. It was therefore protective in the DSS-induced colitis model.

Affymetrix Analysis

Principal component analysis (PCA) was performed on the microarray data to separate the samples in a 3-dimensional way. Control and DSS/HP clustered together, and DSS were separate from this cluster. This PCA therefore indicated that DSS transcriptome profile was very different from the control and DSS/HP profiles, which were very similar. In turn, this indicated that HP was effective in treating the inflammation, as these animals seemed similar to healthy animals.

ANOVA with unequal variance (Welch), P<0.05, asymptotic, all against single condition, Tukey HSD post-hoc was carried out to get a list of differentially expressed genes. This generated a table of 377 genes with differential expression (Table 1 and Table 3).

TABLE 1 Genes with differential expression between DSS and Control and DSS/HP and control in rats given Dextran Sodium Sulphate in water with or without co-treatment with hypothetical protein (HP). Fold change Gene DSS vs DSS/HP vs Gene description symbol Control Control p-value Regenerating islet-derived 3 beta Reg3b 11.400 2.107 0.016 Resistin-like gamma | resistin like Retnlg|Retnlb 3.957 1.556 0.020 beta Sucrase-isomaltase (alpha- Si 3.903 1.347 0.040 glucosidase) Defensin, alpha, 24 Defa24 3.045 1.552 0.026 Hydroxysteroid 11-beta Hsd11b2 −2.002 1.001 0.041 dehydrogenase 2 Hydroxysteroid (17-beta) Hsd17b2 −2.530 −1.603 0.040 dehydrogenase 2 Nuclear receptor subfamily 3, Nr3c2 −1.447 −1.092 0.009 group C, member 2 Gene description GO_biological_process (up to first 10) Regenerating islet- GO:0006953 acute-phase response; GO:0006954 derived 3 beta inflammatory response Resistin-like gamma | resistin like beta Sucrase-isomaltase GO:0005975 carbohydrate metabolic process; (alpha-glucosidase) GO:0007568 aging; GO:0007584 response to nutrient; GO:0008152 metabolic process; GO:0009744 response to sucrose stimulus; GO:0009750 response to fructose stimulus; GO:0032868 response to insulin stimulus; GO:0033189 response to vitamin A; GO:0042594 response to starvation; GO:0051384 response to glucocorticoid stimulus Defensin, alpha, 24 GO:0006952 defense response; GO:0042742 defense response to bacterium Hydroxysteroid 11-beta GO:0001666 response to hypoxia; GO:0002017 dehydrogenase 2 regulation of blood volume by renal aldosterone; GO:0006950 response to stress; GO:0007565 female pregnancy; GO:0008152 metabolic process; GO:0008211 glucocorticoid metabolic process; GO:0032094 response to food; GO:0032868 response to insulin stimulus; GO:0042493 response to drug; GO:0048545 response to steroid hormone stimulus Hydroxysteroid (17-beta) GO:0006694 steroid biosynthetic process; dehydrogenase 2 GO:0032526 response to retinoic acid; GO:0055114 Nuclear receptor GO:0006355 regulation of transcription, DNA- subfamily 1, group D, dependent; GO:0007623 circadian rhythm; member 1 | thyroid GO:0001502 cartilage condensation; GO:0001503 hormone receptor alpha ossification; GO:0001822 kidney development; GO:0001889 liver development; GO:0002155 regulation of thyroid hormone mediated signaling pathway; GO:0006950 response to stress; GO:0007420 brain development; GO:0007611 learning or memory

A heatmap was created of the subset of 377 genes (FIG. 7). This heatmap showed clear clustering of the DSS animals away from the Control and DSS/HP animals, which themselves also clustered separately, albeit not as distant from each other. The overall colour pattern of control and DSS/HP was very similar, while the DSS animals mostly showed inverse fold changes for this gene subset to the other two groups.

Seven of these genes showed comparatively high fold changes compared to controls. Of these seven genes, 4 were up regulated and the other 3 were down regulated with respect to control (Table 1). These fold changes were generally higher for the DSS animals than for the DSS/HP animals. The most affected genes were regenerating islet-derived 3 beta (Reg3b), resistin-like gamma Iresistin like beta (RetnIg|Retnlb), sucrase-isomaltase (alpha-glucosidase) (Si) and defensin alpha 24 (Defa24), which were up regulated and hydroxysteroid 11-beta dehydrogenase 2 (Hsd11b2), hydroxysteroid (17-beta) dehydrogenase 2 (Hsd17b2), and nuclear receptor 1D1I thyroid hormone receptor alpha (Nr1d1|Thra), which were down regulated with respect to the control (Table 1).

Realtime PCR

Expression of inflammation-associated genes in the ascending colon was generally lower in rats treated with DSS and HP than in tissue from rats treated with DSS alone (FIG. 8; Table 2). Reg3 and RELMb expression were in particular greatly reduced as a result of treatment with HP.

TABLE 2 Statistical analysis of inflammation-associated genes (Realtime PCR) in ascending colons from rats given Dextran Sodium Sulphate in water with or without co-treatment with hypothetical protein (HP). DSS vs Control DSS/HP vs Control DSS vs DSS/HP Fold Fold Fold change p-value change p-value change p-value RELM-b 6.61 0.03 1.2 0.17 5.49 0.04 Reg3 61.25 0.04 4.04 0.24 15.15 0.01 Defa24 23.08 0.01 6.37 0.01 3.62 0.22 CXCL10 1.1 0.91 1.78 0.48 −1.63 0.39 TNF −1.16 0.9 2.19 0.54 −2.55 0.11 Hsd −3.17 0.01 −2.28 0.01 −1.39 0.36 IL6 3.2 0.43 1.35 0.81 2.37 0.11

Summary

Hypothetical protein ameliorated moderate DSS-induced colitis. This protection was, in part, linked with reduced expression of pro-inflammatory markers in the gut tissue.

Table 3 details all genes with differential expression between DSS and Control and DSS/HP and control in rats given Dextran Sodium Sulphate in water with or without co-treatment with hypothetical protein (HP).

Fold change DSS vs DSS/HP vs Gene description Gene symbol Control Control p-value GO_biological_process (up to first 10) Regenerating islet-derived 3 beta Reg3b 11.400 2.107 0.016 GO:0006953 acute-phase response; GO:0006954 inflammatory response Resistin-like gamma | resistin like beta Retnlg|Retnlb 3.957 1.556 0.020 Sucrase-isomaltase (alpha-glucosidase) Si 3.903 1.347 0.040 GO:0005975 carbohydrate metabolic process; GO:0007568 aging; GO:0007584 response to nutrient; GO:0008152 metabolic process; GO:0009744 response to sucrose stimulus; GO:0009750 response to fructose stimulus; GO:0032868 response to insulin stimulus; GO:0033189 response to vitamin A; GO:0042594 response to starvation; GO:0051384 response to glucocorticoid stimulus Defensin, alpha, 24 Defa24 3.045 1.552 0.026 GO:0006952 defense response; GO:0042742 defense response to bacterium Matrix Gla protein Mgp 2.223 1.176 0.048 GO:0001503 ossification; GO:0006461 protein complex assembly; GO:0007275 multicellular organismal development; GO:0007584 response to nutrient; GO:0009612 response to mechanical stimulus; GO:0009725 response to hormone stimulus; GO:0030154 cell differentiation; GO:0030324 lung development; GO:0030500 regulation of bone mineralization; GO:0042221 response to chemical stimulus Phospholipase A2, group IIA (platelets, synovial Pla2g2a 2.006 1.262 0.027 GO:0006644 phospholipid metabolic process; GO:0008285 negative regulation of cell fluid) proliferation; GO:0016042 lipid catabolic process; GO:0035019 somatic stem cell maintenance; GO:0042127 regulation of cell proliferation; GO:0046473 phosphatidic acid metabolic process; GO:0050678 regulation of epithelial cell proliferation; GO:0050680 negative regulation of epithelial cell proliferation Gremlin 1, cysteine knot superfamily, homolog Grem1 1.982 1.338 0.010 GO:0001658 branching involved in ureteric bud morphogenesis; GO:0002689 negative (Xenopus laevis) regulation of leukocyte chemotaxis; GO:0006915 apoptosis; GO:0007267 cell-cell signaling; GO:0009887 organ morphogenesis; GO:0009954 proximal/distal pattern formation; GO:0010717 regulation of epithelial to mesenchymal transition; GO:0030308 negative regulation of cell growth; GO:0030326 embryonic limb morphogenesis; GO:0030514 negative regulation of BMP signaling pathway Ribosomal protein L10A | similar to ribosomal Rpl10a| 1.958 1.086 0.033 GO:0006396 RNA processing; GO:0006412 translation; GO:0006414 translational elongation protein L10a RGD1559639| RGD1566137 Hydroxysteroid 11-beta dehydrogenase 1 Hsd11b1 1.907 1.233 0.000 GO:0006278 RNA-dependent DNA replication; GO:0006694 steroid biosynthetic process; GO:0006704 glucocorticoid biosynthetic process; GO:0006713 glucocorticoid catabolic process; GO:0008152 metabolic process; GO:0030324 lung development; GO:0043456 regulation of pentose-phosphate shunt Carbamoyl-phosphate synthetase 1 Cps1 1.858 1.245 0.020 GO:0000050 urea cycle; GO:0005980 glycogen catabolic process; GO:0006541 glutamine metabolic process; GO:0006807 nitrogen compound metabolic process; GO:0014075 response to amine stimulus; GO:0019433 triglyceride catabolic process; GO:0032496 response to lipopolysaccharide; GO:0033762 response to glucagon stimulus; GO:0034201 response to oleic acid; GO:0042493 response to drug Paraoxonase 3 Pon3 1.816 1.358 0.033 GO:0019439 aromatic compound catabolic process; GO:0046395 carboxylic acid catabolic process Ornithine carbamoyltransferase Otc 1.816 1.190 0.032 GO:0000050 urea cycle; GO:0006526 arginine biosynthetic process; GO:0006591 ornithine metabolic process; GO:0008652 cellular amino acid biosynthetic process; GO:0051259 protein oligomerization; GO:0055081 anion homeostasis Leukocyte immunoglobulin-like receptor, subfamily Lilrb4 1.769 1.185 0.013 B, member 4 Cadherin 19, type 2 Cdh19 1.732 1.328 0.001 GO:0007155 cell adhesion; GO:0007156 homophilic cell adhesion Complement factor H Cfh 1.723 1.509 0.031 GO:0006956 complement activation; GO:0030449 regulation of complement activation Vomeronasal 1 receptor, E14 V1re14 1.715 1.369 0.004 GO:0007186 G-protein coupled receptor protein signaling pathway Solute carrier family 25 (mitochondrial carrier; Slc25a4 1.701 1.228 0.010 GO:0015866 ADP transport; GO:0015867 ATP transport; GO:0051935 glutamate uptake adenine nucleotide translocator), member 4 involved in synaptic transmission; GO:0055085 transmembrane transport; GO:0060547 negative regulation of necrotic cell death Immediate early response 3 Ier3 1.692 1.227 0.037 ST3 beta-galactoside alpha-2,3-sialyltransferase 4 St3gal4 1.666 −1.069 0.047 GO:0006486 protein amino acid glycosylation Fc fragment of IgG, low affinity IIa, receptor Fcgr2a| 1.652 1.150 0.013 GO:0001788 antibody-dependent cellular cytotoxicity; GO:0001798 positive regulation of (CD32) | Fc fragment of IgG, low affinity IIb, Fcgr2b| type IIa hypersensitivity; GO:0001805 positive regulation of type III hypersensitivity; receptor (CD32) | Fc gamma receptor II beta | Low LOC498276| GO:0001812 positive regulation of type I hypersensitivity; GO:0001820 serotonin secretion; affinity immunoglobulin gamma Fc region receptor LOC100362543 GO:0006910 phagocytosis, recognition; GO:0006911 phagocytosis, engulfment; GO:0007166 III-like cell surface receptor linked signaling pathway; GO:0021675 nerve development; GO:0030593 neutrophil chemotaxis Eukaryotic translation initiation factor 3, subunit E Eif3e 1.647 1.287 0.025 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; GO:0006413 translational initiation Family with sequence similarity 96, member A Fam96a 1.641 1.277 0.014 GO:0008150 biological_process Peroxisomal membrane protein 3 Pxmp3 1.631 1.093 0.007 GO:0001764 neuron migration; GO:0006699 bile acid biosynthetic process; GO:0007031 peroxisome organization; GO:0007399 nervous system development; GO:0008150 biological_process; GO:0042632 cholesterol homeostasis; GO:0045540 regulation of cholesterol biosynthetic process; GO:0001764 neuron migration; GO:0006699 bile acid biosynthetic process; GO:0007031 peroxisome organization Fibroblast growth factor 15 Fgf15 1.618 1.045 0.005 GO:0001755 neural crest cell migration; GO:0007507 heart development; GO:0008284 positive regulation of cell proliferation; GO:0008543 fibroblast growth factor receptor signaling pathway; GO:0046326 positive regulation of glucose import; GO:0046330 positive regulation of JNK cascade; GO:0070374 positive regulation of ERK1 and ERK2 cascade; GO:0070858 negative regulation of bile acid biosynthetic process Phospholamban Pln 1.616 1.194 0.021 GO:0002026 regulation of the force of heart contraction; GO:0006816 calcium ion transport// non-traceable author statement; GO:0006874 cellular calcium ion homeostasis; GO:0045822 negative regulation of heart contraction; GO:0048738 cardiac muscle tissue development; GO:0051924 regulation of calcium ion transport Suppressor of cytokine signaling 3 Socs3 1.613 1.157 0.007 GO:0001558 regulation of cell growth; GO:0001666 response to hypoxia; GO:0001932 regulation of protein amino acid phosphorylation; GO:0007165 signal transduction; GO:0007243 intracellular protein kinase cascade; GO:0007259 JAK-STAT cascade; GO:0007568 aging; GO:0009408 response to heat; GO:0009617 response to bacterium; GO:0009725 response to hormone stimulus PQ loop repeat containing 3 Pqlc3 1.608 1.073 0.037 Midkine Mdk 1.600 1.032 0.045 GO:0000087 M phase of mitotic cell cycle; GO:0007275 multicellular organismal development; GO:0009611 response to wounding; GO:0009725 response to hormone stimulus; GO:0016477 cell migration; GO:0030154 cell differentiation; GO:0030325 adrenal gland development; GO:0042493 response to drug; GO:0051384 response to glucocorticoid stimulus; GO:0051781 positive regulation of cell division MOB1, Mps One Binder kinase activator-like 3 Mobkl3 1.593 1.310 0.047 GO:0006810 transport (yeast) Nuclear factor, interleukin 3 regulated Nfil3 1.589 1.579 0.041 GO:0006355 regulation of transcription, DNA-dependent; GO:0048511 rhythmic process Alpha-2u globulin PGCL1 | alpha-2u-globulin (L LOC259246| 1.586 −1.100 0.021 GO:0006810 transport type) | alpha-2u globulin PGCL2 | alpha2u globulin | LOC298116| alpha-2u globulin PGCL3 | alpha 2U globulin LOC298109| LOC298111| LOC259244| LOC366380 Tp53rk binding protein Tprkb 1.580 1.187 0.018 Similar to protein C33A12.3 RGD1359508 1.574 1.141 0.013 V-ral simian leukemia viral oncogene homolog A Rala 1.563 1.175 0.005 GO:0000910 cytokinesis; GO:0007165 signal transduction; GO:0007264 small GTPase (ras related) mediated signal transduction; GO:0007265 Ras protein signal transduction; GO:0017157 regulation of exocytosis; GO:0031532 actin cytoskeleton reorganization; GO:0051491 positive regulation of filopodium assembly; GO:0051665 membrane raft localization Hematopoietic prostaglandin D synthase Hpgds 1.539 1.220 0.009 GO:0001516 prostaglandin biosynthetic process; GO:0006633 fatty acid biosynthetic process; GO:0006693 prostaglandin metabolic process Forkhead box E3 Foxe3 1.519 1.131 0.024 GO:0001654 eye development; GO:0006350 transcription; GO:0006355 regulation of transcription, DNA-dependent; GO:0006366 transcription from RNA polymerase II promoter; GO:0008150 biological_process; GO:0045449 regulation of transcription; GO:0048468 cell development; GO:0050679 positive regulation of epithelial cell proliferation Complement component 1, s subcomponent C1s 1.513 1.170 0.006 GO:0006508 proteolysis; GO:0006958 complement activation, classical pathway; GO:0010001 glial cell differentiation; GO:0045087 innate immune response; GO:0051591 response to cAMP Reticulocalbin 2, EF-hand calcium binding domain Rcn2 1.512 1.223 0.035 Solute carrier family 7 (cationic amino acid Slc7a9 1.500 1.047 0.046 GO:0006865 amino acid transport; GO:0055085 transmembrane transport; GO:0015804 transporter, y+ system), member 9 neutral amino acid transport Butyrylcholinesterase Bche 1.488 1.042 0.019 GO:0007584 response to nutrient; GO:0007612 learning; GO:0019695 choline metabolic process; GO:0042493 response to drug; GO:0043279 response to alkaloid; GO:0050805 negative regulation of synaptic transmission; GO:0051384 response to glucocorticoid stimulus; GO:0051593 response to folic acid SFT2 domain containing 1 Sft2d1 1.487 1.125 0.023 GO:0015031 protein transport; GO:0016192 vesicle-mediated transport TCF3 (E2A) fusion partner Tfpt 1.475 1.165 0.002 GO:0006917 induction of apoptosis UDP-Gal:betaGlcNAc beta 1,4- B4galt4 1.466 1.188 0.008 GO:0005975 carbohydrate metabolic process galactosyltransferase, polypeptide 4 Somatostatin Sst 1.460 1.139 0.020 GO:0001101 response to acid; GO:0006972 hyperosmotic response; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0009408 response to heat; GO:0010243 response to organic nitrogen; GO:0030334 regulation of cell migration; GO:0042493 response to drug; GO:0043200 response to amino acid stimulus; GO:0048545 response to steroid hormone stimulus Lin-7 homolog C (C. elegans) Lin7c 1.459 1.195 0.005 GO:0006887 exocytosis; GO:0007269 neurotransmitter secretion Glycoprotein (transmembrane) nmb Gpnmb 1.452 1.100 0.036 GO:0001649 osteoblast differentiation; GO:0007155 cell adhesion; GO:0030282 bone mineralization Coiled-coil-helix-coiled-coil-helix domain Chchd4| 1.449 1.121 0.033 GO:0015031 protein transport; GO:0055085 transmembrane transport containing 4 | similar to coiled-coil-helix-coiled- LOC685505 coil-helix domain containing 4 Olfactory receptor 63 Olr63 1.445 1.147 0.029 GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Proline-rich acidic protein 1 Prap1 1.444 1.055 0.035 Immunoglobulin superfamily, member 6 Igsf6 1.443 1.108 0.045 Ly49 inhibitory receptor 9 | hypothetical protein Ly49i9| 1.440 1.026 0.034 LOC497796 | killer cell lectin-like receptor, LOC497796| subfamily A, member 17 | similar to Klra17| immunoreceptor Ly49si3 RGD1561306 Allograft inflammatory factor 1 Aif1 1.431 1.107 0.010 GO:0001934 positive regulation of protein amino acid phosphorylation; GO:0010629 negative regulation of gene expression; GO:0014739 positive regulation of muscle hyperplasia; GO:0030335 positive regulation of cell migration; GO:0031668 cellular response to extracellular stimulus; GO:0032870 cellular response to hormone stimulus; GO:0034097 response to cytokine stimulus; GO:0042116 macrophage activation; GO:0043066 negative regulation of apoptosis; GO:0045429 positive regulation of nitric oxide biosynthetic process Legumain Lgmn 1.427 1.268 0.003 GO:0006508 proteolysis; GO:0040015 negative regulation of multicellular organism growth Brain expressed X-linked 2 | brain expressed gene 1 | Bex2| 1.420 1.194 0.043 GO:0006915 apoptosis; GO:0007049 cell cycle; GO:0002052 positive regulation of neuroblast brain expressed gene 4 Bex1| proliferation; GO:0007275 multicellular organismal development; GO:0007399 nervous Bex4 system development; GO:0030154 cell differentiation; GO:0045665 negative regulation of neuron differentiation; GO:0048011 nerve growth factor receptor signaling pathwav Tumor suppressor candidate 3 Tusc3 1.419 1.145 0.049 GO:0045454 cell redox homeostasis ATP synthase, H+ transporting, mitochondrial F0 Atp5h| 1.415 1.072 0.036 GO:0006811 ion transport; GO:0015986 ATP synthesis coupled proton transport; complex, subunit d | ATP synthase, H+ transporting, Atp5hl1 GO:0015992 proton transport; GO:0046034 ATP metabolic process mitochondrial F0 complex, subunit d-like 1 C-type lectin domain family 10, member A Clec10a 1.413 −1.051 0.034 Sodium channel, voltage-gated, type VII, alpha Scn7a 1.412 1.274 0.017 GO:0006811 ion transport; GO:0006814 sodium ion transport; GO:0055085 transmembrane transport Cd55 1.412 1.065 0.015 GO:0007204 elevation of cytosolic calcium ion concentration Galactokinase 2 Galk2 1.409 1.182 0.000 GO:0006012 galactose metabolic process; GO:0008152 metabolic process; GO:0046835 carbohydrate phosphorylation Necdin homolog (mouse) Ndn 1.402 1.174 0.004 GO:0001764 neuron migration; GO:0006355 regulation of transcription, DNA-dependent; GO:0007409 axonogenesis; GO:0007413 axonal fasciculation; GO:0007417 central nervous system development; GO:0007585 respiratory gaseous exchange; GO:0008347 glial cell migration; GO:0019233 sensory perception of pain; GO:0048011 nerve growth factor receptor signaling pathway; GO:0048666 neuron development BUD31 homolog (S. cerevisiae) | pentatricopeptide Bud31| 1.401 1.098 0.047 repeat domain 1 Ptcd1 Proenkephalin Penk 1.394 1.073 0.017 GO:0001662 behavioral fear response; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007218 neuropeptide signaling pathway; GO:0007610 behavior; GO:0019233 sensory perception of pain Musculoskeletal, embryonic nuclear protein 1 Mustn1 1.394 1.074 0.031 GO:0030326 embryonic limb morphogenesis; GO:0042060 wound healing; GO:0042246 tissue regeneration EGF-like module containing, mucin-like, hormone Emr4 1.380 1.175 0.025 GO:0007218 neuropeptide signaling pathway receptor-like sequence 4 Testis specific X-linked gene Tsx 1.378 1.245 0.000 Lecithin-retinol acyltransferase Lrat 1.369 1.058 0.004 GO:0006776 vitamin A metabolic process; GO:0007601 visual perception; GO:0009790 (phosphatidylcholine-retinol-O-acyltransferase) embryonic development; GO:0042572 retinol metabolic process; GO:0050896 response to stimulus Integrin, alpha 1 Itga1 1.366 1.089 0.013 GO:0000187 activation of MAPK activity; GO:0006936 muscle contraction; GO:0007155 cell adhesion; GO:0007229 integrin-mediated signaling pathway; GO:0030593 neutrophil chemotaxis; GO:0042311 vasodilation; GO:0043525 positive regulation of neuron apoptosis; GO:0045123 cellular extravasation; GO:0048812 neuron projection morphogenesis; GO:0060326 cell chemotaxis Stathmin-like 3 Stmn3 1.355 1.164 0.005 GO:0007019 microtubule depolymerization; GO:0031122 cytoplasmic microtubule organization; GO:0031175 neuron projection development; GO:0032314 regulation of Rac GTPase activity; GO:0035021 negative regulation of Rac protein signal transduction; GO:0051493 regulation of cytoskeleton organization Family with sequence similarity 12, member B Fam12b 1.344 1.134 0.003 (epididymal) Mitochondrial ribosomal protein L13 Mrpl13 1.344 1.089 0.022 GO:0006412 translation Similar to RIKEN cDNA 1700023M03 RGD1305457 1.344 1.078 0.000 Growth differentiation factor 9 Gdf9 1.343 1.019 0.029 GO:0001555 oocyte growth; GO:0030308 negative regulation of cell growth Olfactory receptor 826 | olfactory receptor 825 | Olr826| 1.334 1.264 0.001 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of olfactory receptor 829 Olr825| chemical stimulus involved in sensory perception of smell; GO:0007165 signal transduction Olr829 Oxidized low density lipoprotein (lectin-like) Olr1 1.333 1.081 0.022 GO:0006954 inflammatory response; GO:0006955 immune response; GO:0007155 cell receptor 1 adhesion; GO:0007159 leukocyte cell-cell adhesion; GO:0008219 cell death; GO:0042157 lipoprotein metabolic process; GO:0042542 response to hydrogen peroxide Heat shock protein alpha 2 Hspa2 1.325 1.044 0.023 GO:0006950 response to stress; GO:0007275 multicellular organismal development; GO:0007283 spermatogenesis; GO:0030154 cell differentiation Membrane-spanning 4-domains, subfamily A, Ms4a2 1.321 1.129 0.031 GO:0006954 inflammatory response; GO:0007165 signal transduction; GO:0007166 cell member 2 (Fc fragment of IgE, high affinity I, surface receptor linked signaling pathway; GO:0007202 activation of phospholipase C receptor for; beta polypeptide) activity; GO:0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; GO:0043306 positive regulation of mast cell degranulation; GO:0050663 cytokine secretion; GO:0051279 regulation of release of sequestered calcium ion into cytosol Mesenchyme homeobox 2 Meox2 1.320 1.087 0.013 GO:0001525 angiogenesis; GO:0001757 somite specification; GO:0006355 regulation of transcription, DNA-dependent; GO:0007275 multicellular organismal development; GO:0007519 skeletal muscle tissue development; GO:0060021 palate development; GO:0060173 limb development Angiopoietin-like 3 Angptl3 1.319 1.166 0.002 GO:0006071 glycerol metabolic process; GO:0006631 fatty acid metabolic process; GO:0006644 phospholipid metabolic process; GO:0007160 cell-matrix adhesion; GO:0007165 signal transduction; GO:0008203 cholesterol metabolic process; GO:0009395 phospholipid catabolic process; GO:0009725 response to hormone stimulus; GO:0010519 negative regulation of phospholipase activity; GO:0019915 lipid storage Phosphotriesterase related Pter 1.318 1.091 0.008 GO:0009056 catabolic process G protein-coupled receptor 119 Gpr119 1.317 1.164 0.036 GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0030073 insulin secretion Similar to 14-3-3 protein sigma | stratifin LOC298795| 1.309 1.084 0.036 GO:0000079 regulation of cyclin-dependent protein kinase activity; GO:0001836 release of Sfn cytochrome c from mitochondria; GO:0008285 negative regulation of cell proliferation; GO:0008630 DNA damage response, signal transduction resulting in induction of apoptosis; GO:0030216 keratinocyte differentiation; GO:0030307 positive regulation of cell growth; GO:0043154 negative regulation of caspase activity; GO:0043588 skin development; GO:0043616 keratinocyte proliferation; GO:0000079 regulation of cyclin-dependent protein kinase activity Serpine1 mRNA binding protein 1 Serbp1 1.307 1.136 0.041 GO:0045767 regulation of anti-apoptosis Granzyme F Gzmf 1.300 1.043 0.027 GO:0006508 proteolysis Tissue factor pathway inhibitor (lipoprotein- Tfpi 1.298 1.198 0.000 GO:0007596 blood coagulation; GO:0007598 blood coagulation, extrinsic pathway associated coagulation inhibitor) Fibroblast growth factor 3 Fgf3 1.294 1.138 0.036 GO:0001759 induction of an organ; GO:0008284 positive regulation of cell proliferation; GO:0008543 fibroblast growth factor receptor signaling pathway; GO:0048538 thymus development Secreted and transmembrane 1A Sectm1a 1.292 1.096 0.003 GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB cascade Ubiquitin-conjugating enzyme RGD69425 1.288 1.059 0.040 GO:0008150 biological_process; GO:0043687 post-translational protein modification; GO:0051246 regulation of protein metabolic process Neuropeptide W Npw 1.287 1.009 0.029 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007218 neuropeptide signaling pathway; GO:0007631 feeding behavior LOC362526 1.282 1.026 0.014 Olfactory receptor 1075 Olr1075 1.279 −1.179 0.027 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Myelin protein zero-like 1 Mpzl1 1.278 1.269 0.001 Keratin 18 Krt18 1.276 1.124 0.048 GO:0006915 apoptosis; GO:0008150 biological_process; GO:0033209 tumor necrosis factor- mediated signaling pathway; GO:0043000 Golgi to plasma membrane CFTR protein transport; GO:0043066 negative regulation of apoptosis Choline phosphotransferase 1 Chpt1 1.273 1.198 0.033 GO:0006656 phosphatidylcholine biosynthetic process; GO:0006663 platelet activating factor biosynthetic process; GO:0008654 phospholipid biosynthetic process Neurogenic differentiation 1 Neurod1 1.271 1.152 0.020 GO:0003326 pancreatic A cell fate commitment; GO:0003329 pancreatic PP cell fate commitment; GO:0006355 regulation of transcription, DNA-dependent; GO:0007263 nitric oxide mediated signal transduction; GO:0007275 multicellular organismal development; GO:0007399 nervous system development; GO:0009749 response to glucose stimulus; GO:0009952 anterior/posterior pattern formation; GO:0021549 cerebellum development; GO:0030073 insulin secretion Fibroblast growth factor 2 Fgf2 1.264 1.032 0.042 GO:0000186 activation of MAPKK activity; GO:0000189 nuclear translocation of MAPK; GO:0001525 angiogenesis; GO:0001658 branching involved in ureteric bud morphogenesis; GO:0001759 induction of an organ; GO:0001934 positive regulation of protein amino acid phosphorylation; GO:0002042 cell migration involved in sprouting angiogenesis; GO:0006355 regulation of transcription, DNA-dependent; GO:0006700 C21-steroid hormone biosynthetic process; GO:0006915 apoptosis Fin bud initiation factor homolog (zebrafish) Fibin 1.264 1.014 0.001 Olfactory receptor 7 Olr7 1.261 1.228 0.011 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Sterol O-acyltransferase 2 Soat2 1.256 −1.037 0.016 GO:0007584 response to nutrient; GO:0008202 steroid metabolic process; GO:0008203 cholesterol metabolic process; GO:0033344 cholesterol efflux; GO:0034379 very-low-density lipoprotein particle assembly; GO:0034435 cholesterol esterification Neurexin 1 Nrxn1 1.256 1.071 0.022 GO:0007268 synaptic transmission; GO:0007269 neurotransmitter secretion; GO:0007416 synapse assembly; GO:0051290 protein heterotetramerization MARCKS-like 1 Marcksl1 1.251 1.104 0.033 GO:0008284 positive regulation of cell proliferation; GO:0016192 vesicle-mediated transport Calcium/calmodulin-dependent protein kinase II Camk2n1 1.251 1.151 0.024 GO:0007268 synaptic transmission inhibitor 1 Armadillo repeat containing, X-linked 1 Armcx1 1.247 1.042 0.003 Protocadherin beta 2 Pcdhb2 1.244 1.090 0.037 GO:0007155 cell adhesion; GO:0007156 homophilic cell adhesion ELAV (embryonic lethal, abnormal vision, Elavl2 1.242 −1.022 0.041 Drosophila)-like 2 (Hu antigen B) DNA-damage regulated autophagy modulator 2 | Dram2| 1.239 1.088 0.013 GO:0006915 apoptosis; GO:0006917 induction of apoptosis similar to CG4025-PA LOC689412 Proteolipid protein 1 Plp1 1.238 1.183 0.019 GO:0007229 integrin-mediated signaling pathway; GO:0008366 axon ensheathment; GO:0010001 glial cell differentiation; GO:0022010 myelination in the central nervous system; GO:0042552 myelination; GO:0042759 long-chain fatty acid biosynthetic process; GO:0048469 cell maturation Aspartoacylase Aspa 1.237 1.012 0.036 GO:0008152 metabolic process; GO:0022010 myelination in the central nervous system; GO:0048714 positive regulation of oligodendrocyte differentiation First gene upstream of Nt5dc3 LOC362863 1.232 1.198 0.037 PRKC, apoptosis, WT1, regulator Pawr 1.232 1.140 0.049 GO:0006915 apoptosis; GO:0030889 negative regulation of B cell proliferation; GO:0042094 interleukin-2 biosynthetic process; GO:0042130 negative regulation of T cell proliferation; GO:0042986 positive regulation of amyloid precursor protein biosynthetic process; GO:0045449 regulation of transcription; GO:0050860 negative regulation of T cell receptor signaling pathway Glutamate receptor, ionotropic, AMPA4 Gria4 1.231 1.181 0.036 GO:0007268 synaptic transmission Fumarylacetoacetate hydrolase domain containing 1 Fahd1 1.229 1.152 0.039 GO:0008152 metabolic process McKusick-Kaufman syndrome Mkks 1.225 1.178 0.010 GO:0007286 spermatid development; GO:0007608 sensory perception of smell; GO:0008150 biological_process; GO:0009296 flagellum assembly; GO:0021756 striatum development; GO:0021766 hippocampus development; GO:0021987 cerebral cortex development; GO:0035058 sensory cilium assembly; GO:0035176 social behavior; GO:0042384 cilium assembly Protein kinase inhibitor, gamma Pkig 1.223 1.226 0.017 GO:0000122 negative regulation of transcription from RNA polymerase II promoter; GO:0006469 negative regulation of protein kinase activity; GO:0007165 signal transduction; GO:0042308 negative regulation of protein import into nucleus Cholecystokinin B receptor Cckbr 1.222 1.103 0.036 GO:0001821 histamine secretion; GO:0002209 behavioral defense response; GO:0006915 apoptosis; GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007204 elevation of cytosolic calcium ion concentration; GO:0007586 digestion; GO:0008284 positive regulation of cell proliferation; GO:0032230 positive regulation of synaptic transmission, GABAergic; GO:0032868 response to insulin stimulus RAS-like family 11 member B Rasl11b 1.221 1.156 0.028 GO:0007165 signal transduction; GO:0007264 small GTPase mediated signal transduction Galanin receptor 1 Galr1 1.219 1.117 0.047 GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007189 activation of adenylate cyclase activity by G-protein signaling pathway Potassium voltage gated channel, Shab-related Kcnb1 1.217 1.040 0.038 GO:0006811 ion transport; GO:0006813 potassium ion transport; GO:0051259 protein subfamily, member 1 oligomerization; GO:0055085 transmembrane transport Protein disulfide isomerase family A, member 4 Pdia4 1.216 1.159 0.037 GO:0045454 cell redox homeostasis Myosin, light polypeptide 1 Myl1 1.215 1.128 0.024 GO:0060048 cardiac muscle contraction Persephin Pspn 1.213 1.255 0.006 GO:0001658 branching involved in ureteric bud morphogenesis Tumor necrosis factor (ligand) superfamily, member Tnfsf13 1.212 1.228 0.001 GO:0002426 immunoglobulin production in mucosal tissue; GO:0002636 positive regulation 13 of germinal center formation; GO:0006955 immune response; GO:0008150 biological_process; GO:0008284 positive regulation of cell proliferation; GO:0016064 immunoglobulin mediated immune response; GO:0048298 positive regulation of isotype switching to IgA isotypes; GO:0050776 regulation of immune response ADP-ribosylation factor interacting protein 1 Arfip1 1.211 1.039 0.027 GO:0006886 intracellular protein transport; GO:0050708 regulation of protein secretion Zinc finger, MYND-tvpe containing 19 Zmynd19 1.211 1.043 0.035 Centrosomal protein 70 kDa Cep70 1.210 1.158 0.024 Ribosomal L24 domain containing 1 Rsl24d1 1.210 1.139 0.035 GO:0006412 translation; GO:0042254 ribosome biogenesis Ring finger protein 133 Rnf133 1.209 1.157 0.018 GO:0051865 protein autoubiquitination Plasma glutamate carboxypeptidase Pgcp 1.205 1.147 0.044 GO:0006508 proteolysis; GO:0042246 tissue regeneration DnaJ (Hsp40) homolog, subfamily A, member 1 Dnaja1 1.199 1.320 0.014 GO:0006457 protein folding; GO:0007283 spermatogenesis; GO:0009408 response to heat; GO:0030317 sperm motility; GO:0030521 androgen receptor signaling pathway; GO:0042769 DNA damage response, detection of DNA damage Transmembrane and coiled-coil domains 1 Tmco1 1.198 1.057 0.011 GO:0008150 biological process Arrestin, beta 1 Arrb1 1.196 1.204 0.002 GO:0000187 activation of MAPK activity; GO:0002031 G-protein coupled receptor internalization; GO:0002032 desensitization of G-protein coupled receptor protein signaling pathway by arrestin; GO:0006366 transcription from RNA polymerase II promoter; GO:0006892 post-Golgi vesicle-mediated transport; GO:0006897 endocytosis; GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007188 G-protein signaling, coupled to cAMP nucleotide second messenger//; GO:0007600 sensory perception Dystonia 1 Dyt1 1.193 1.043 0.002 GO:0006457 protein folding; GO:0006979 response to oxidative stress; GO:0051085 chaperone mediated protein folding requiring cofactor Latrophilin 3 Lphn3 1.191 1.172 0.025 GO:0007218 neuropeptide signaling pathway; GO:0007420 brain development FK506 binding protein 14 Fkbp14 1.190 1.332 0.022 GO:0006457 protein folding Nitric oxide synthase 2, inducible Nos2 1.188 1.001 0.021 GO:0001542 ovulation from ovarian follicle; GO:0001666 response to hypoxia; GO:0001935 endothelial cell proliferation; GO:0001974 blood vessel remodeling; GO:0006527 arginine catabolic process; GO:0006801 superoxide metabolic process; GO:0006809 nitric oxide biosynthetic process; GO:0007165 signal transduction; GO:0007199 G-protein signaling, coupled to cGMP nucleotide second messenger; GO:0007243 intracellular protein kinase cascade Olfactory receptor 1105 Olr1105 1.187 −1.050 0.026 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Heat shock protein beta 2 Hspb2 1.186 −1.117 0.041 GO:0007525 somatic muscle development; GO:0009408 response to heat Uncoupling protein 1 (mitochondrial, proton carrier) Ucp1 1.185 1.100 0.009 GO:0006091 generation of precursor metabolites and energy; GO:0006839 mitochondrial transport; GO:0015992 proton transport; GO:0032870 cellular response to hormone stimulus; GO:0044253 positive regulation of multicellular organismal metabolic process; GO:0048545 response to steroid hormone stimulus; GO:0050873 brown fat cell differentiation; GO:0055085 transmembrane transport Ankyrin repeat and SOCS box-containing 2 Asb2 1.182 1.117 0.037 WD repeat domain 31 Wdr31 1.182 1.041 0.036 Neurexophilin 4 Nxph4 1.180 −1.046 0.047 Keratin 82 Krt82 1.178 1.063 0.043 Feline leukemia virus subgroup C cellular receptor Flvcr2 1.177 −1.071 0.028 GO:0055085 transmembrane transport family, member 2 Alpha-2u globulin PGCL4 | major urinary protein 4 | Obp3| 1.176 −1.185 0.030 GO:0006810 transport alpha-2u globulin PGCL3 | alpha-2u globulin Mup4| PGCL1 | alpha2u globulin | alpha-2u globulin LOC259244| PGCL2 | alpha 2U globulin LOC259246| LOC298111| LOC298109| LOC366380 Reelin Rein 1.176 1.055 0.037 GO:0000904 cell morphogenesis involved in differentiation; GO:0001764 neuron migration; GO:0007411 axon guidance; GO:0007417 central nervous system development; GO:0007420 brain development; GO:0007626 locomotory behavior; GO:0010001 glial cell differentiation; GO:0018108 peptidyl-tyrosine phosphorylation; GO:0021511 spinal cord patterning; GO:0021800 cerebral cortex tangential migration Vesicle-associated membrane protein 7 Vamp7 1.175 1.049 0.048 GO:0006888 ER to Golgi vesicle-mediated transport; GO:0006906 vesicle fusion; GO:0006911 phagocytosis, engulfment; GO:0008333 endosome to lysosome transport; GO:0015031 protein transport; GO:0016044 cellular membrane organization; GO:0016192 vesicle-mediated transport; GO:0017156 calcium ion-dependent exocytosis; GO:0043308 eosinophil degranulation; GO:0043312 neutrophil degranulation Plasminogen Plg 1.175 −1.022 0.037 GO:0006915 apoptosis; GO:0006917 induction of apoptosis; GO:0007596 blood coagulation; GO:0042246 tissue regeneration; GO:0045445 myoblast differentiation; GO:0046716 muscle cell homeostasis; GO:0048771 tissue remodeling; GO:0051603 proteolysis involved in cellular protein catabolic process; GO:0051918 negative regulation of fibrinolysis; GO:0051919 positive regulation of fibrinolysis Family with sequence similarity 131, member B Fam131b 1.173 1.085 0.020 Cholinergic receptor, nicotinic, beta 2 (neuronal) Chmb2 1.169 1.112 0.004 GO:0001508 regulation of action potential; GO:0001661 conditioned taste aversion; GO:0001666 response to hypoxia; GO:0006811 ion transport; GO:0006816 calcium ion transport; GO:0006939 smooth muscle contraction; GO:0007165 signal transduction; GO:0007271 synaptic transmission, cholinergic; GO:0007601 visual perception; GO:0007605 sensory perception of sound Dynein light chain LC8-type 1 Dynll1 1.169 1.153 0.033 GO:0006809 nitric oxide biosynthetic process; GO:0007017 microtubule-based process; GO:0008633 activation of pro-apoptotic gene products; GO:0042133 neurotransmitter metabolic process; GO:0042326 negative regulation of phosphorylation Kinesin family member 27 Kif27 1.167 1.078 0.005 GO:0007018 microtubule-based movement LOC362793 RGD1307315 1.165 1.033 0.021 Unc-50 homolog (C. elegans) Unc50 1.163 1.035 0.044 GO:0007166 cell surface receptor linked signaling pathway; GO:0015031 protein transport Sonic hedgehog Shh 1.163 1.202 0.010 GO:0001525 angiogenesis; GO:0001569 patterning of blood vessels; GO:0001570 vasculogenesis; GO:0001656 metanephros development; GO:0001658 branching involved in ureteric bud morphogenesis; GO:0001666 response to hypoxia; GO:0001708 cell fate specification; GO:0001755 neural crest cell migration; GO:0001822 kidney development; GO:0001841 neural tube formation Histidine decarboxylase Hdc 1.162 1.041 0.044 GO:0001692 histamine metabolic process; GO:0006519 cellular amino acid and derivative metabolic process; GO:0006547 histidine metabolic process; GO:0006548 histidine catabolic process; GO:0019752 carboxylic acid metabolic process; GO:0042423 catecholamine biosynthetic process Olfactory receptor 1593 Olr1593 1.162 1.083 0.037 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Zinc finger protein 354A Zfp354a 1.160 1.051 0.007 GO:0000122 negative regulation of transcription from RNA polymerase II promoter; GO:0001666 response to hypoxia; GO:0001822 kidney development; GO:0006355 regulation of transcription, DNA-dependent; GO:0007275 multicellular organismal development; GO:0007576 nucleolar fragmentation; GO:0051593 response to folic acid Tumor protein p63 Tp63 1.157 1.048 0.026 GO:0000122 negative regulation of transcription from RNA polymerase II promoter; GO:0001302 replicative cell aging; GO:0001501 skeletal system development; GO:0001736 establishment of planar polarity; GO:0001738 morphogenesis of a polarized epithelium; GO:0001942 hair follicle development; GO:0002053 positive regulation of mesenchymal cell proliferation; GO:0002064 epithelial cell development; GO:0006915 apoptosis; GO:0006916 anti-apoptosis Histone cluster 1, H1t Hist1h1t 1.155 1.034 0.015 GO:0006334 nucleosome assembly; GO:0007275 multicellular organismal development; GO:0007283 spermatogenesis; GO:0007339 binding of sperm to zona pellucida; GO:0030154 cell differentiation; GO:0030317 sperm motility Disabled homolog 1 (Drosophila) Dab1 1.154 −1.073 0.018 GO:0001764 neuron migration; GO:0007162 negative regulation of cell adhesion; GO:0007264 small GTPase mediated signal transduction; GO:0007275 multicellular organismal development; GO:0007399 nervous system development; GO:0007420 brain development; GO:0021589 cerebellum structural organization; GO:0021795 cerebral cortex cell migration; GO:0021799 cerebral cortex radially oriented cell migration; GO:0021813 cell- cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration Leucine rich repeat containing 66 Lrrc66 1.154 1.139 0.045 Neuronal PAS domain protein 4 Npas4 1.154 1.095 0.015 GO:0007165 signal transduction; GO:0045941 positive regulation of transcription; GO:0045944 positive regulation of transcription from RNA polymerase II promoter; GO:0045944 positive regulation of transcription from RNA polymerase II promoter N-acetylneuraminic acid phosphatase Nanp 1.154 1.165 0.042 GO:0005975 carbohydrate metabolic process; GO:0008152 metabolic process; GO:0046380 N-acetylneuraminate biosynthetic process MAD2L1 binding protein Mad211bp 1.152 1.111 0.004 GO:0007093 mitotic cell cycle checkpoint; GO:0007096 regulation of exit from mitosis Neuromedin S NMS 1.152 −1.015 0.045 GO:0006940 regulation of smooth muscle contraction; GO:0007218 neuropeptide signaling pathway; GO:0045475 locomotor rhythm Transmembrane protease, serine 8 (intestinal) Tmprss8 1.149 1.203 0.035 GO:0006508 proteolysis; GO:0006811 ion transport; GO:0006814 sodium ion transport Myoglobin Mb 1.149 1.036 0.015 GO:0001666 response to hypoxia; GO:0006810 transport; GO:0007507 heart development; GO:0009725 response to hormone stimulus; GO:0015671 oxygen transport; GO:0031444 slow-twitch skeletal muscle fiber contraction; GO:0042542 response to hydrogen peroxide; GO:0043353 enucleate erythrocyte differentiation; GO:0050873 brown fat cell differentiation Similar to RIKEN cDNA 1500031L02 RGD621352 1.145 1.411 0.006 Dehydrogenase/reductase (SDR family) member 7 Dhrs7 1.145 −1.013 0.046 GO:0055114 oxidation reduction Nuclear pore associated protein Npap60 1.143 −1.073 0.033 GO:0001841 neural tube formation; GO:0015031 protein transport; GO:0046907 intracellular transport; GO:0051028 mRNA transport; GO:0055085 transmembrane transport Olfactory receptor 484 Olr484 1.141 1.355 0.016 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Torsin family 3, member A Tor3a 1.140 1.088 0.020 GO:0051085 chaperone mediated protein folding requiring cofactor Similar to Protein C20orf103 precursor RGD1306991 1.139 −1.041 0.041 Similar to RAN protein RGD1306195 1.138 1.112 0.014 GO:0006886 intracellular protein transport; GO:0006913 nucleocytoplasmic transport; GO:0007165 signal transduction Natriuretic peptide receptor A/guanylate cyclase A Npr1 1.138 1.050 0.034 GO:0006182 cGMP biosynthetic process; GO:0006468 protein amino acid phosphorylation; (atrionatriuretic peptide receptor A) GO:0007166 cell surface receptor linked signaling pathway; GO:0007168 receptor guanylyl cyclase signaling pathway; GO:0008217 regulation of blood pressure; GO:0030828 positive regulation of cGMP biosynthetic process; GO:0042417 dopamine metabolic process Olfactory receptor 174 Olr174 1.138 1.294 0.040 GO:0007186 G-protein coupled receptor protein signaling pathway ; GO:0050911 detection of chemical stimulus involved in sensory perception of smell NADH dehydrogenase (ubiquinone) 1 alpha Ndufaf3 1.131 −1.084 0.042 GO:0032981 mitochondrial respiratory chain complex I assembly I assembly subcomplex, assembly factor 3 Interleukin 6 signal transducer Il6st 1.128 1.061 0.001 GO:0005977 glycogen metabolic process; GO:0006642 triglyceride mobilization; GO:0007165 signal transduction; GO:0007259 JAK-STAT cascade; GO:0007584 response to nutrient; GO:0008284 positive regulation of cell proliferation; GO:0008593 regulation of Notch signaling pathway; GO:0014911 positive regulation of smooth muscle cell migration; GO:0019221 cytokine-mediated signaling pathway; GO:0030307 positive regulation of cell growth Synuclein, alpha (non A4 component of amyloid Snca 1.127 1.096 0.005 GO:0001774 microglial cell activation; GO:0001921 positive regulation of receptor recycling; precursor) GO:0001956 positive regulation of neurotransmitter secretion; GO:0001963 synaptic transmission, dopaminergic; GO:0006631 fatty acid metabolic process; GO:0006638 neutral lipid metabolic process; GO:0006644 phospholipid metabolic process; GO:0006916 anti- apoptosis; GO:0007006 mitochondrial membrane organization; GO:0008344 adult locomotory behavior Interferon regulatory factor 3 Irf3 1.127 1.166 0.011 GO:0006355 regulation of transcription, DNA-dependent; GO:0007249 I-kappaB kinase/NF- kappaB cascade; GO:0009617 response to bacterium; GO:0031663 lipopolysaccharide- mediated signaling pathway; GO:0032496 response to lipopolysaccharide; GO:0043330 response to exogenous dsRNA; GO:0045351 type I interferon biosynthetic process Asialoglycoprotein receptor 1 Asgr1 1.121 1.051 0.028 GO:0006897 endocytosis; GO:0031668 cellular response to extracellular stimulus Heat shock 105 kDa/110 kDa protein 1 Hsph1 1.120 1.358 0.036 GO:0006950 response to stress; GO:0051085 chaperone mediated protein folding requiring cofactor Actin, gamma 2, smooth muscle, enteric Actg2 1.117 1.070 0.008 GO:0006936 muscle contraction Similar to putative protein, with at least 9 RGD1309228 1.111 1.099 0.007 transmembrane domains, of eukaryotic origin (43.9 kD) (2G415) Transient receptor potential cation channel, Trpv2 1.111 1.060 0.018 GO:0006811 ion transport; GO:0006816 calcium ion transport; GO:0009266 response to subfamily V, member 2 temperature stimulus; GO:0009408 response to heat; GO:0055085 transmembrane transport Glutathione S-transferase, theta 2 Gstt2 1.108 1.123 0.033 GO:0006749 glutathione metabolic process Adenosine A3 receptor Adora3 1.099 −1.150 0.048 GO:0001973 adenosine receptor signaling pathway; GO:0002553 histamine secretion by mast cell; GO:0002687 positive regulation of leukocyte migration; GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0014061 regulation of norepinephrine secretion; GO:0014068 positive regulation of phosphoinositide 3-kinase cascade; GO:0043306 positive regulation of mast cell degranulation; GO:0050729 positive regulation of inflammatory response; GO:0050850 positive regulation of calcium-mediated signaling Sarcolipin Sln 1.087 1.355 0.038 GO:0051924 regulation of calcium ion transport N-myc downstream regulated gene 4 Ndrg4 1.087 1.105 0.010 Gypsy retrotransposon integrase 1 Gin1 1.086 1.054 0.025 GO:0015074 DNA integration ATP-binding cassette, sub-family G (WHITE), Abcg311| 1.084 1.064 0.043 member 3-like 1 | ATP-binding cassette, sub-family Abcg312| G (WHITE), member 3-like 2 | similar to ATP- RGD1564709| binding cassette, sub-family G (WHITE), member 3 LOC360997 Oxytocin, prepropeptide | arginine vasopressin Oxt| 1.084 −1.112 0.013 GO:0001696 gastric acid secretion; GO:0001975 response to amphetamine; GO:0002027 Avp regulation of heart rate; GO:0002125 maternal aggressive behavior; GO:0003077 negative regulation of diuresis; GO:0003079 positive regulation of natriuresis; GO:0006950 response to stress; GO:0007204 elevation of cytosolic calcium ion concentration; GO:0007507 heart development; GO:0007565 female pregnancy Thimet oligopeptidase 1 Thop1 1.080 −1.013 0.049 GO:0006508 proteolysis; GO:0006518 peptide metabolic process; GO:0007243 intracellular protein kinase cascade cAMP responsive element binding protein 3 Creb3 1.078 1.137 0.021 GO:0006355 regulation of transcription, DNA-dependent Peroxisomal biogenesis factor 12 Pex12 1.071 1.149 0.001 GO:0007031 peroxisome organization; GO:0015031 protein transport; GO:0016558 protein import into peroxisome matrix Endothelin receptor type A | endothelin-1 receptor- Ednra| 1.071 1.130 0.009 GO:0001569 patterning of blood vessels; GO:0001666 response to hypoxia; GO:0001701 in like LOC100366209 utero embryonic development; GO:0001934 positive regulation of protein amino acid phosphorylation; GO:0007165 signal transduction; GO:0007204 elevation of cytosolic calcium ion concentration; GO:0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; GO:0007507 heart development; GO:0007585 respiratory gaseous exchange; GO:0008217 regulation of blood pressure Mk1 1.068 −1.152 0.038 GO:0030036 actin cytoskeleton organization Protein geranylgeranyltransferase type I, beta Pggt1b 1.062 1.162 0.039 GO:0008284 positive regulation of cell proliferation; GO:0018348 protein amino acid subunit geranylgeranylation; GO:0034097 response to cytokine stimulus; GO:0045787 positive regulation of cell cycle; GO:0051774 negative regulation of nitric-oxide synthase 2 biosynthetic process; GO:0051789 response to protein stimulus Olfactory receptor 1356 Olr1356 1.061 1.323 0.021 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Immunity-related GTPase family, cinema 1 Irgc1 1.060 −1.124 0.017 Distal-less homeobox 5 Dlx5 1.050 −1.140 0.008 GO:0001649 osteoblast differentiation; GO:0001958 endochondral ossification; GO:0006355 regulation of transcription, DNA-dependent; GO:0007275 multicellular organismal development; GO:0007399 nervous system development; GO:0007409 axonogenesis; GO:0007411 axon guidance; GO:0008283 cell proliferation; GO:0030326 embryonic limb morphogenesis; GO:0030855 epithelial cell differentiation RELT-like 2 | FCH and double SH3 domains 1 Rell2| 1.047 −1.088 0.041 GO:0010811 positive regulation of cell-substrate adhesion Fchsd1 Membrane magnesium transporter 2 Mmgt2 1.047 1.171 0.025 GO:0006810 transport; GO:0006824 cobalt ion transport; GO:0006825 copper ion transport; GO:0006828 manganese ion transport; GO:0015674 di-, tri-valent inorganic cation transport; GO:0015675 nickel ion transport; GO:0015693 magnesium ion transport STEAP family member 3 Steap3 1.046 1.177 0.004 GO:0006811 ion transport; GO:0006826 iron ion transport; GO:0006915 apoptosis; GO:0006917 induction of apoptosis; GO:0007049 cell cycle; GO:0009306 protein secretion; GO:0055114 oxidation reduction Sialidase 2 (cytosolic sialidase) Neu2 1.030 1.134 0.023 GO:0008152 metabolic process; GO:0010831 positive regulation of myotube differentiation; GO:0045471 response to ethanol; GO:0045663 positive regulation of myoblast differentiation Spermatogenesis associated 6 Spata6 1.028 1.057 0.045 GO:0007275 multicellular organismal development; GO:0007283 spermatogenesis; GO:0030154 cell differentiation Fibroblast growth factor 20 Fgf20 1.027 −1.096 0.044 GO:0008284 positive regulation of cell proliferation; GO:0008543 fibroblast growth factor receptor signaling pathway; GO:0016049 cell growth; GO:0030154 cell differentiation; GO:0060113 inner ear receptor cell differentiation Cholinergic receptor, nicotinic, alpha 9 Chrna9 1.022 −1.124 0.006 GO:0006812 cation transport; GO:0006816 calcium ion transport; GO:0007204 elevation of cytosolic calcium ion concentration; GO:0007605 sensory perception of sound; GO:0042472 inner ear morphogenesis; GO:0050910 detection of mechanical stimulus involved in sensory perception of sound Coagulation factor II (thrombin) receptor F2r 1.005 1.345 0.007 GO:0000186 activation of MAPKK activity; GO:0002248 connective tissue replacement during inflammatory response; GO:0006919 activation of caspase activity; GO:0006954 inflammatory response; GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007205 activation of protein kinase C activity by G- protein coupled receptor protein signaling pathway; GO:0007260 tyrosine phosphorylation of STAT protein; GO:0007262 STAT protein nuclear translocation; GO:0007529 establishment of synaptic specificity at neuromuscular junction Potassium channel, subfamily K, member 1 Kcnk1 1.004 1.241 0.015 GO:0006811 ion transport; GO:0006813 potassium ion transport; GO:0035094 response to nicotine Ameloblastin Ambn −1.000 −1.046 0.025 Adhesion molecule with Ig like domain 3 Amigo 3 −1.023 1.147 0.022 GO:0007155 cell adhesion; GO:0007157 heterophilic cell-cell adhesion; GO:0007399 nervous system development Ankyrin repeat and SOCS box-containing 6 Asb6 −1.028 −1.072 0.015 ATPase, H transporting, lysosomal V1 subunit B2 Atp6v1b2 −1.039 1.046 0.011 GO:0006811 ion transport; GO:0007035 vacuolar acidification; GO:0015986 ATP synthesis coupled proton transport; GO:0015992 proton transport; GO:0030641 regulation of cellular pH; GO:0046034 ATP metabolic process Myeloid/lymphoid or mixed-lineage leukemia Mllt10 −1.041 −1.001 0.023 GO:0008150 biological_process (trithorax homolog, Drosophila); translocated to, 10 Phosphorylase kinase, beta Phkb −1.042 1.078 0.009 GO:0005976 polysaccharide metabolic process; GO:0005977 glycogen metabolic process Olfactory receptor 1409 Olr1409 −1.059 −1.105 0.038 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell MIF4G domain containing Mif4gd −1.063 −1.109 0.002 GO:0006417 regulation of translation; GO:0016070 RNA metabolic process Olfactory receptor 44 Olr44 −1.073 −1.122 0.039 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Sulfatase modifying factor 2 Sumf2 −1.077 −1.088 0.034 WD repeat domain 45 Wdr45 −1.078 1.120 0.049 Syndecan binding protein Sdcbp −1.080 1.170 0.008 GO:0007265 Ras protein signal transduction Bemardinelli-Seip congenital lipodystrophy 2 Bscl2 −1.082 −1.006 0.047 GO:0008150 biological_process homolog (human) Dehydrogenase/reductase (SDR family) member 1 Dhrs1 −1.083 1.116 0.006 GO:0055114 oxidation reduction Polymerase (DNA directed), gamma Polg −1.089 −1.102 0.029 GO:0006264 mitochondrial DNA replication; GO:0006287 base-excision repair, gap-filling; GO:0007568 aging Protein O-fucosyltransferase 1 Pofut1 −1.091 1.038 0.026 GO:0001525 angiogenesis; GO:0001756 somitogenesis; GO:0005975 carbohydrate metabolic process; GO:0006004 fucose metabolic process; GO:0006493 protein amino acid O-linked glycosylation; GO:0007219 Notch signaling pathway; GO:0007399 nervous system development; GO:0007507 heart development; GO:0008150 biological process Outer dense fiber of sperm tails 2 Odf2 −1.098 −1.005 0.044 GO:0007286 spermatid development Nuclear prelamin A recognition factor-like Narfl −1.099 −1.006 0.017 GO:0001666 response to hypoxia; GO:0016226 iron-sulfur cluster assembly; GO:0032364 oxygen homeostasis; GO:0045449 regulation of transcription Solute carrier family 6 (neurotransmitter transporter, Slc6a4 −1.105 −1.065 0.038 GO:0001504 neurotransmitter uptake; GO:0006837 serotonin transport; GO:0007626 serotonin), member 4 locomotory behavior; GO:0009636 response to toxin; GO:0015844 monoamine transport; GO:0021794 thalamus development; GO:0051610 serotonin uptake Acyl-Coenzyme A oxidase 3, pristanoyl Acox3 −1.106 −1.081 0.001 GO:0006629 lipid metabolic process; GO:0006631 fatty acid metabolic process; GO:0006635 fatty acid beta-oxidation; GO:0033540 fatty acid beta-oxidation using acyl-CoA oxidase; GO:0055114 oxidation reduction Shroom family member 2 Shroom2 −1.115 1.191 0.035 GO:0000902 cell morphogenesis; GO:0007275 multicellular organismal development; GO:0016477 cell migration; GO:0030835 negative regulation of actin filament depolymerization; GO:0032438 melanosome organization; GO:0045217 cell-cell junction maintenance; GO:0051017 actin filament bundle assemblv Similar to RIKEN cDNA A730011L01 gene LOC498029 −1.115 −1.077 0.023 GO:0006281 DNA repair Neuropeptide FF receptor 1 Npffr1 −1.117 −1.111 0.024 GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway Kelch-like 36 (Drosophila) Klhl36 −1.119 −1.021 0.014 Phosphatidylinositol glycan anchor biosynthesis, Pigs −1.128 1.007 0.033 GO:0006506 GPI anchor biosynthetic process; GO:0016255 attachment of GPI anchor to class S protein PDZ and LIM domain 1 Pdlim1 −1.131 1.111 0.049 GO:0001666 response to hypoxia; GO:0045449 regulation of transcription Alpha-1-B glycoprotein A1bg −1.132 −1.048 0.005 WD repeat domain 7 Wdr7 −1.133 −1.041 0.017 Protein O-linked mannose betal,2-N- Pomgnt1 −1.135 −1.056 0.012 GO:0006487 protein amino acid N-linked glycosylation; GO:0006493 protein amino acid O- acetylglucosaminyltransferase linked glycosylation; GO:0008150 biological process Fibroblast growth factor 11 Fgf11 −1.135 −1.162 0.016 DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 Ddx24 −1.139 1.006 0.027 Heterogeneous nuclear ribonucleoprotein H1 Hnrph1 −1.143 1.100 0.040 GO:0006396 RNA processing Rho-related BTB domain containing 2 Rhobtb2 −1.145 −1.024 0.013 GO:0007264 small GTPase mediated signal transduction Ring finger protein 135 Rnf135 −1.147 −1.045 0.013 GO:0006270 DNA-dependent DNA replication initiation; GO:0007264 small GTPase mediated signal transduction; GO:0047497 mitochondrion transport along microtubule Vaccinia related kinase 3 Vrk3 −1.150 1.011 0.046 GO:0006468 protein amino acid phosphorylation; GO:0032516 positive regulation of phosphoprotein phosphatase activity; GO:0070373 negative regulation of ERK1 and ERK2 cascade Cardiotrophin-like cytokine factor 1 Clcf1 −1.150 −1.144 0.029 GO:0007166 cell surface receptor linked signaling pathway; GO:0007259 JAK-STAT cascade; GO:0030183 B cell differentiation Prostate tumor overexpressed 1 Ptov1 −1.154 −1.014 0.050 GO:0045449 regulation of transcription Mitogen activated protein kinase kinase kinase 1 Map3k1 −1.158 −1.106 0.008 GO:0000165 MAPKKK cascade; GO:0000186 activation of MAPKK activity; GO:0000209 protein polyubiquitination; GO:0006468 protein amino acid phosphorylation; GO:0006970 response to osmotic stress; GO:0007179 transforming growth factor beta receptor signaling pathway; GO:0007249 I-kappaB kinase/NF-kappaB cascade; GO:0007254 JNK cascade; GO:0007256 activation of JNKK activity; GO:0007257 activation of JUN kinase activity Calcium homeostasis endoplasmic reticulum protein | Cherp| −1.160 −1.040 0.018 GO:0006396 RNA processing; GO:0006874 cellular calcium ion homeostasis; GO:0008285 similar to 1700030K09Rik protein RGD1311847 negative regulation of cell proliferation Progestin and adipoQ receptor family member III Paqr3 −1.161 −1.063 0.016 Glioma tumor suppressor candidate region gene 2 Gltscr2 −1.162 −1.123 0.012 Poly(rC) binding protein 2 Pcbp2 −1.162 −1.015 0.014 GO:0008380 RNA splicing THO complex 5 Thoc5 −1.163 −1.025 0.036 GO:0006397 mRNA processing; GO:0006406 mRNA export from nucleus; GO:0006810 transport; GO:0008150 biological_process; GO:0008380 RNA splicing; GO:0030154 cell differentiation; GO:0045650 negative regulation of macrophage differentiation; GO:0046784 intronless viral mRNA export from host nucleus; GO:0051028 mRNA transport Glycine-, glutamate-, thienylcyclohexylpiperidine- LOC246295 −1.165 1.035 0.045 binding protein Family with sequence similarity 113, member A Fam113a −1.171 1.022 0.049 Leucine rich repeat (in FLU) interacting protein 1 Lrrfip1 −1.175 1.000 0.048 GO:0045449 regulation of transcription AlkB, alkylation repair homolog 3 (E. coli) Alkbh3 −1.177 −1.138 0.001 GO:0006281 DNA repair; GO:0055114 oxidation reduction Amyloid beta (A4) precursor protein-binding, Apbb3 −1.181 1.016 0.018 family B, member 3 Cyclin-dependent kinase inhibitor 2B (pl5, inhibits Cdkn2b −1.185 −1.104 0.017 GO:0000079 regulation of cyclin-dependent protein kinase activity; GO:0000086 G2/M CDK4) transition of mitotic cell cycle; GO:0007050 cell cycle arrest; GO:0008285 negative regulation of cell proliferation; GO:0014070 response to organic cyclic substance; GO:0030219 megakaryocyte differentiation; GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway; GO:0030858 positive regulation of epithelial cell differentiation; GO:0031575 G1/S transition checkpoint; GO:0031668 cellular response to extracellular stimulus CD2-associated protein Cd2ap −1.189 −1.089 0.039 GO:0016337 cell-cell adhesion; GO:0016477 cell migration; GO:0043161 proteasomal ubiquitin-dependent protein catabolic process; GO:0048259//regulation of receptor-mediated endocytosis ATPase, Na+/K+ transporting, beta 1 polypeptide Atp1b1 −1.192 −1.020 0.036 GO:0001666 response to hypoxia; GO:0006754 ATP biosynthetic process; GO:0006811 ion transport; GO:0006813 potassium ion transport; GO:0006814 sodium ion transport; GO:0030001 metal ion transport Ring finger protein 114 Rnf114 −1.193 1.005 0.050 GO:0007275 multicellular organismal development; GO:0007283 spermatogenesis; GO:0030154 cell differentiation Inositol polyphosphate phosphatase-like 1 Inppl1 −1.198 −1.022 0.046 GO:0006006 glucose metabolic process; GO:0007420 brain development; GO:0008156 negative regulation of DNA replication; GO:0008285 negative regulation of cell proliferation; GO:0009791 post-embryonic development; GO:0010629 negative regulation of gene expression; GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway; GO:0010977 negative regulation of neuron projection development; GO:0032868 response to insulin stimulus; GO:0032957 inositol trisphosphate metabolic process TAO kinase 2 Taok2 −1.200 −1.058 0.010 GO:0000186 activation of MAPKK activity; GO:0006468 protein amino acid phosphorylation; GO:0006950 response to stress; GO:0008360 regulation of cell shape; GO:0030036 actin cytoskeleton organization; GO:0046330 positive regulation of JNK cascade; GO:0048041 focal adhesion assembly; GO:0000186 activation of MAPKK activity Dynamin 2 Dnm2 −1.200 −1.085 0.036 GO:0006892 post-Golgi vesicle-mediated transport; GO:0006897 endocytosis; GO:0006898 receptor-mediated endocytosis; GO:0016044 cellular membrane organization; GO:0031623 receptor internalization; GO:0033572 transferrin transport Calcium channel, voltage-dependent, beta 3 subunit Cacnb3 −1.200 1.009 0.029 GO:0006811 ion transport; GO:0006816 calcium ion transport; GO:0050852 T cell receptor signaling pathway Similar to chromosome 1 open reading frame 172 RGD1303271 −1.201 −1.049 0.048 Pre-B-cell leukemia homeobox 2 Pbx2 −1.202 −1.007 0.019 GO:0006355 regulation of transcription, DNA-dependent; GO:0009954 proximal/distal pattern formation; GO:0030326 embiyonic limb morphogenesis; GO:0045944 positive regulation of transcription from RNA polymerase II promoter SCY1-like 1 (S. cerevisiae) | latent transforming Scyl1| −1.204 1.032 0.034 GO:0006468 protein amino acid phosphorylation; GO:0006890 retrograde vesicle-mediated growth factor beta binding protein 3 Ltbp3 transport, Golgi to ER; GO:0016192 vesicle-mediated transport Olfactory receptor 1765 Olr1765 −1.206 −1.436 0.003 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Transmembrane BAX inhibitor motif containing 6 Tmbim6 −1.209 −1.048 0.006 GO:0007283 spermatogenesis; GO:0030324 lung development; GO:0043066 negative regulation of apoptosis Solute carrier organic anion transporter family, Slco2b1 −1.210 1.027 0.030 GO:0001889 liver development; GO:0006811 ion transport; GO:0015721 bile acid and bile member 2b1 salt transport; GO:0071718 sodium-independent icosanoid transport Trace amine-associated receptor 8c Taar8c −1.210 1.130 0.011 GO:0007165 signal transduction; GO:0007186 G-protein coupled receptor protein signaling pathway Transmembrane protein, adipocyte asscociated 1 Tpra1 −1.211 −1.019 0.033 DiGeorge syndrome critical region gene 2 Dgcr2 −1.211 −1.046 0.036 GO:0042493 response to drug Casein kinase 1, delta | solute carrier family 16, Csnk1d| −1.211 −1.042 0.021 GO:0000278 mitotic cell cycle; GO:0006468 protein amino acid phosphorylation; member 3 (monocarboxylic acid transporter 4) Slc16a3 GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process; GO:0032922 circadian regulation of gene expression; GO:0042752 regulation of circadian rhythm; GO:0006090 pyruvate metabolic process; GO:0015711 organic anion transport; GO:0055085 transmembrane transport Scaffold attachment factor B Safb −1.219 −1.003 0.016 GO:0006355 regulation of transcription, DNA-dependent; GO:0030520 estrogen receptor signaling pathway; GO:0040007 growth; GO:0042445 hormone metabolic process; GO:0050684 regulation of mRNA processing MAP/microtubule affinity-regulating kinase 2 Mark2 −1.219 −1.025 0.044 GO:0006468 protein amino acid phosphorylation; GO:0006979 response to oxidative stress; GO:0007243 intracellular protein kinase cascade; GO:0007275 multicellular organismal development; GO:0030154 cell differentiation; GO:0045197 establishment or maintenance of epithelial cell apical/basal polarity Era (G-protein)-like 1 (E. coli) Eral1 −1.219 1.006 0.040 RT1 class I, locus CE12 | RT1 class I, locus1 | RT1 RT1- −1.220 −1.156 0.002 GO:0002474 antigen processing and presentation of peptide antigen via MHC class I; class I, locus CE14 CE12| GO:0006955 immune response; GO:0019882 antigen processing and presentation RT1- CE14 Serine incorporator 3 Serinc3 −1.220 1.055 0.021 GO:0006658 phosphatidylserine metabolic process; GO:0006665 sphingolipid metabolic process; GO:0006917 induction of apoptosis; GO:0015825 L-serine transport; GO:0051347 positive regulation of transferase activity Cancer susceptibility candidate 3 Casc3 −1.225 −1.024 0.048 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; GO:0006397 mRNA processing; GO:0006417 regulation of translation; GO:0006810 transport; GO:0006950 response to stress; GO:0008298 intracellular mRNA localization; GO:0008380 RNA splicing; GO:0051028 mRNA transport DAB2 interacting protein Dab2ip −1.233 −1.016 0.038 GO:0007165 signal transduction; GO:0051056 regulation of small GTPase mediated signal transduction Gamma-glutamyl transferase 6 Ggt6 −1.233 −1.024 0.018 GO:0006750 glutathione biosynthetic process Fatty acid desaturase 1 Fads1 −1.233 −1.192 0.021 GO:0006636 unsaturated fatty acid biosynthetic process; GO:0006810 transport; GO:0006950 response to stress; GO:0007568 aging; GO:0007584 response to nutrient; GO:0009267 cellular response to starvation; GO:0009744 response to sucrose stimulus; GO:0010033 response to organic substance; GO:0014070 response to organic cyclic substance; GO:0019369 arachidonic acid metabolic process PTK2B protein tyrosine kinase 2 beta Ptk2b −1.233 −1.101 0.009 GO:0000165 MAPKKK cascade; GO:0000302 response to reactive oxygen species; GO:0001525 angiogenesis; GO:0001556 oocyte maturation; GO:0001666 response to hypoxia; GO:0006468 protein amino acid phosphorylation; GO:0006800 oxygen and reactive oxygen species metabolic process; GO:0006950 response to stress; GO:0006970 response to osmotic stress; GO:0007015 actin filament organization RAD23 homolog A (S. cerevisiae) Rad23a −1.234 −1.089 0.008 GO:0006289 nucleotide-excision repair; GO:0006974 response to DNA damage stimulus; GO:0043161 proteasomal ubiquitin-dependent protein catabolic process GDP dissociation inhibitor 1 Gdi1 −1.235 −1.013 0.025 GO:0007264 small GTPase mediated signal transduction; GO:0015031 protein transport; GO:0043087 regulation of GTPase activity Solute carrier family 15, member 4 Slc15a4 −1.237 −1.100 0.029 GO:0006857 oligopeptide transport; GO:0015031 protein transport; GO:0015817 histidine transport DALR anticodon binding domain containing 3 Dalrd3 −1.242 1.008 0.026 GO:0006420 arginyl-tRNA aminoacylation Axin 1 Axin1 −1.244 −1.077 0.006 GO:0007275 multicellular organismal development; GO:0007605 sensory perception of sound; GO:0010800 positive regulation of peptidyl-threonine phosphorylation; GO:0016055 Wnt receptor signaling pathway; GO:0030163 protein catabolic process; GO:0030178 negative regulation of Wnt receptor signaling pathway; GO:0031398 positive regulation of protein ubiquitination; GO:0033138 positive regulation of peptidyl-serine phosphorylation; GO:0046330 positive regulation of JNK cascade; GO:0060070 Wnt receptor signaling pathway through beta-catenin ATG7 autophagy related 7 homolog (S. cerevisiae) Atg7 −1.247 −1.107 0.010 GO:0001889 liver development; GO:0006497 protein amino acid lipidation; GO:0006520 cellular amino acid metabolic process; GO:0006914 autophagy; GO:0006996 organelle organization; GO:0007628 adult walking behavior; GO:0008152 metabolic process; GO:0009791 post-embryonic development; GO:0015031 protein transport; GO:0016044 cellular membrane organization General transcription factor III Gtf2i −1.247 1.033 0.046 GO:0009790 embiyonic development; GO:0051481 reduction of cytosolic calcium ion concentration Phosphatidylinositol glycan anchor biosynthesis, Pigv −1.253 1.010 0.005 GO:0006506 GPI anchor biosynthetic process; GO:0016254 preassembly of GPI anchor in ER class V membrane Anterior pharynx defective 1 homolog A (C. Aph1a −1.255 −1.029 0.046 GO:0001656 metanephros development; GO:0006509 membrane protein ectodomain elegans) proteolysis; GO:0006915 apoptosis; GO:0007220 Notch receptor processing; GO:0008624 induction of apoptosis by extracellular signals; GO:0016485 protein processing; GO:0031293 membrane protein intracellular domain proteolysis; GO:0042987 amyloid precursor protein catabolic process; GO:0043085 positive regulation of catalytic activity Purinergic receptor P2X, ligand-gated ion channel 4 P2rx4 −1.260 −1.135 0.017 GO:0002028 regulation of sodium ion transport; GO:0006809 nitric oxide biosynthetic process; GO:0006810 transport; GO:0006811 ion transport; GO:0006816 calcium ion transport; GO:0007165 signal transduction; GO:0008217 regulation of blood pressure; GO:0010524 positive regulation of calcium ion transport into cytosol; GO:0010614 negative regulation of cardiac muscle hypertrophy; GO:0019228 regulation of action potential in neuron Secretory carrier membrane protein 2 Scamp2 −1.262 1.071 0.018 GO:0006886 intracellular protein transport; GO:0006897 endocytosis; GO:0015031 protein transport Bcl2-like 1 Bcl211 −1.264 −1.205 0.024 GO:0001541 ovarian follicle development; GO:0001666 response to hypoxia; GO:0001701 in utero embiyonic development; GO:0001836 release of cytochrome c from mitochondria; GO:0006915 apoptosis; GO:0006916 anti-apoptosis; GO:0006950 response to stress; GO:0006979 response to oxidative stress; GO:0007281 germ cell development; GO:0007283 spermatogenesis Olfactory receptor 1614 Olr1614 −1.267 −1.411 0.004 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell LUC7-like (S. cerevisiae) Luc71 −1.270 1.061 0.043 Telomerase associated protein 1 Tepl −1.271 −1.012 0.016 GO:0000722 telomere maintenance via recombination; GO:0000722 telomere maintenance via recombination; GO:0007004 telomere maintenance via telomerase Serine/threonine kinase 39, STE20/SPS1 homolog Stk39 −1.272 −1.061 0.030 GO:0006468 protein amino acid phosphorylation; GO:0043268 positive regulation of (yeast) potassium ion transport CREB binding protein Crebbp −1.272 −1.102 0.002 GO:0006355 regulation of transcription, DNA-dependent; GO:0008283 cell proliferation; GO:0016573 histone acetylation; GO:0018076 N-terminal peptidyl-lysine acetylation; GO:0030718 germ-line stem cell maintenance; GO:0033261 regulation of S phase; GO:0045449 regulation of transcription; GO:0045893 positive regulation of transcription, DNA-dependent; GO:0045941 positive regulation of transcription; GO:0045944 positive regulation of transcription from RNA polvmerase II promoter Serine/threonine kinase 40 Stk40 −1.272 −1.073 0.016 GO:0006468 protein amino acid phosphorylation Protein kinase N1 Pkn1 −1.274 −1.095 0.035 GO:0006468 protein amino acid phosphorylation; GO:0006972 hyperosmotic response; GO:0007165 signal transduction Ligase III, DNA, ATP-dependent Lig3 −1.276 −1.089 0.035 GO:0006260 DNA replication; GO:0006281 DNA repair; GO:0006310 DNA recombination; GO:0033151 V(D)J recombination Post-GPI attachment to proteins 2 Pgap2 −1.277 1.012 0.026 GO:0006916 anti-apoptosis; GO:0006974 response to DNA damage stimulus; GO:0042770 DNA damage response, signal transduction Glucagon Gcg −1.280 −1.140 0.021 GO:0006109 regulation of carbohydrate metabolic process; GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0007188 G-protein signaling, coupled to cAMP nucleotide second messenger; GO:0009755 hormone-mediated signaling pathway; GO:0019216 regulation of lipid metabolic process; GO:0019538 protein metabolic process; GO:0032099 negative regulation of appetite; GO:0050796 regulation of insulin secretion CDC42 small effector 1 Cdc42se1 −1.280 −1.105 0.010 GO:0006909 phagocytosis; GO:0008360 regulation of cell shape Solute carrier family 25 (mitochondrial carrier, Slc25a3 −1.282 1.010 0.025 GO:0055085 transmembrane transport phosphate carrier), member 3 Ubiquitin-associated protein 1 Ubap1 −1.284 −1.090 0.006 ATP citrate lyase Acly −1.292 −1.138 0.025 GO:0006084 acetyl-CoA metabolic processt assay; GO:0006085 acetyl-CoA biosynthetic process; GO:0006101 citrate metabolic process; GO:0006629 lipid metabolic process; GO:0006633 fatty acid biosynthetic process; GO:0008152 metabolic process; GO:0044262 cellular carbohydrate metabolic process Potassium channel, subfamily K, member 6 | Kcnk6| −1.294 1.142 0.019 GO:0006811 ion transport; GO:0006813 potassium ion transport; GO:0000398 nuclear CWC15 spliceosome-associated protein homolog Cwc15| mRNA splicing, via spliceosome; GO:0008150 biological_process; GO:0008380 RNA (S. cerevisiae) | family with sequence similarity 35, Fam35a splicing member A Inositol (myo)-1(or 4)-monophosphatase 2 Impa2 −1.294 −1.024 0.018 GO:0008150 biological process; GO:0046855 inositol phosphate dephosphorylation Transmembrane protein 171 Tmem171 −1.296 1.129 0.022 Zinc finger, DHHC-type containing 23 Zdhhc23 −1.301 −1.025 0.002 A kinase (PRKA) anchor protein 1 Akap1 −1.301 1.061 0.022 GO:0010614 negative regulation of cardiac muscle hypertrophy; GO:0010738 regulation of protein kinase A signaling cascade; GO:0032869 cellular response to insulin stimulus; GO:0035308 negative regulation of protein amino acid dephosphorylation; GO:0051534 negative regulation of NFAT protein import into nucleus; GO:0070887 cellular response to chemical stimulus Shisa homolog 5 (Xenopus laevis) Shisa5 −1.302 1.022 0.010 GO:0006915 apoptosis; GO:0006917 induction of apoptosis; GO:0043123 positive regulation of I-kappaB kinase Phosphatidic acid phosphatase type 2c Ppap2c −1.306 −1.145 0.048 Nuclear RNA export factor 1 Nxf1 −1.307 1.174 0.026 GO:0006405 RNA export from nucleus; GO:0006406 mRNA export from nucleus; GO:0006810 transport; GO:0016973 poly(A)+ mRNA export from nucleus; GO:0051028 mRNA transport Fas-activated serine/threonine kinase Fastk −1.308 −1.082 0.001 GO:0006915 apoptosis Ring finger protein 160 Rnf160 −1.317 1.091 0.042 PCTAIRE protein kinase 1 Pctk1 −1.318 −1.126 0.029 GO:0006468 protein amino acid phosphorylation Prickle homolog 3 (Drosophila) Prickle3 −1.326 −1.096 0.042 Solute carrier family 9 (sodium/hydrogen Slc9a3 −1.333 1.233 0.025 GO:0002028 regulation of sodium ion transport; GO:0006812 cation transport; GO:0006814 exchanger), member 3 sodium ion transport; GO:0006885 regulation of pH; GO:0006898 receptor-mediated endocytosis; GO:0007623 circadian rhythm; GO:0051384 response to glucocorticoid stimulus; GO:0055085 transmembrane transport CDP-diacylglycerol synthase 1 Cds1 −1.339 −1.064 0.014 GO:0008654 phospholipid biosynthetic process Trinucleotide repeat containing 6B Tnrc6b −1.342 −1.089 0.040 Cytochrome P450, family 2, subfamily d, Cyp2d4| −1.347 −1.127 0.001 GO:0008202 steroid metabolic process; GO:0009804 coumarin metabolic process; polypeptide 4 | cytochrome P450, family 2, Cyp2d5 GO:0009820 alkaloid metabolic process; GO:0009822 alkaloid catabolic process; subfamily d, polypeptide 5 GO:0009892 negative regulation of metabolic process; GO:0010033 response to organic substance; GO:0016098 monoterpenoid metabolic process; GO:0017144 drug metabolic process; GO:0019369 arachidonic acid metabolic process; GO:0033076 isoquinoline alkaloid metabolic process Hypothetical protein MGC: 72616 RGD735175 −1.347 −1.059 0.021 Basic helix-loop-helix family, member e40 Bhlhe40 −1.347 −1.158 0.022 GO:0007399 nervous system development; GO:0007623 circadian rhythm; GO:0009416 response to light stimulus; GO:0009649 entrainment of circadian clock; GO:0045892 negative regulation of transcription, DNA-dependent; GO:0048168 regulation of neuronal synaptic plasticity Phosphatidylinositol 4-kinase, catalytic, alpha Pi4ka −1.348 −1.089 0.009 GO:0046854 phosphoinositide phosphorylation; GO:0048015 phosphoinositide-mediated signaling Similar to 2310044H10Rik protein MGC93975 −1.351 −1.168 0.001 CDP-diacylglycerol synthase (phosphatidate Cds2 −1.354 1.015 0.031 GO:0008654 phospholipid biosynthetic process cytidylyltransferase) 2 Prolyl endopeptidase-like Prepl −1.354 1.006 0.045 GO:0006508 proteolysis B-cell translocation gene 1, anti-proliferative Btg1 −1.360 −1.130 0.043 GO:0006479 protein amino acid methylation; GO:0006979 response to oxidative stress; GO:0007283 spermatogenesis; GO:0007286 spermatid development; GO:0008285 negative regulation of cell proliferation; GO:0042981 regulation of apoptosis; GO:0043434 response to peptide hormone stimulus; GO:0045603 positive regulation of endothelial cell differentiation; GO:0045663 positive regulation of myoblast differentiation; GO:0045766 positive regulation of angiogenesis Claudin 3 Cldn3 −1.373 −1.030 0.031 GO:0001666 response to hypoxia; GO:0016338 calcium-independent cell-cell adhesion Serine/threonine kinase 38 Stk38 −1.375 −1.058 0.006 GO:0006464 protein modification process; GO:0006468 protein amino acid phosphorylation; GO:0007243 intracellular protein kinase cascade; GO:0008150 biological process Mucin and cadherin like Mucdhl −1.375 −1.064 0.009 GO:0007155 cell adhesion Thyroid hormone receptor interactor 10 Trip10 −1.377 −1.103 0.011 GO:0006897 endocytosis; GO:0042538 hyperosmotic salinity response Solute carrier family 44, member 1 Slc44a1 −1.381 −1.043 0.010 GO:0015871 choline transport Mitofusin 2 Mfn2 −1.382 −1.103 0.034 GO:0001825 blastocyst formation; GO:0006626 protein targeting to mitochondrion; GO:0007006 mitochondrial membrane organization; GO:0007050 cell cycle arrest; GO:0008053 mitochondrial fusion; GO:0008285 negative regulation of cell proliferation; GO:0046580 negative regulation of Ras protein signal transduction; GO:0048593 camera-type eye morphogenesis; GO:0048662 negative regulation of smooth muscle cell proliferation; GO:0051646 mitochondrion localization Solute carrier family 9 (sodium/hydrogen Slc9a3r1 −1.388 −1.041 0.037 GO:0016055 Wnt receptor signaling pathway; GO:0030643 cellular phosphate ion exchanger), member 3 regulator 1 homeostasis ATP-binding cassette, sub-family B (MDR/TAP), Abcb6 −1.390 1.002 0.008 GO:0006810 transport; GO:0055085 transmembrane transport member 6 Spermatogenesis associated 2 Spata2 −1.390 −1.165 0.039 Sphingomyelin synthase 2 Sgms2 −1.398 −1.072 0.022 GO:0006629 lipid metabolic process; GO:0006665 sphingolipid metabolic process; GO:0006686 sphingomyelin biosynthetic process Ras homolog gene family, member T2 Rhot2 −1.404 1.018 0.049 GO:0006915 apoptosis; GO:0007264 small GTPase mediated signal transduction; GO:0019725 cellular homeostasis; GO:0047497 mitochondrion transport along microtubule V-erb-b2 erythroblastic leukemia viral oncogene Erbb2 −1.417 −1.065 0.047 GO:0001889 liver development; GO:0007165 signal transduction; GO:0007166 cell surface homolog 2, neuro/glioblastoma derived oncogene receptor linked signaling pathway; GO:0007169 transmembrane receptor protein tyrosine homolog (avian) kinase signaling pathway; GO:0007399 nervous system development; GO:0007417 central nervous system development; GO:0007422 peripheral nervous system development; GO:0007507 heart development; GO:0007519 skeletal muscle tissue development; GO:0007528 neuromuscular junction development Integrin alpha FG-GAP repeat containing 3 Itfg3 −1.420 −1.003 0.039 Endothelin 2 Edn2 −1.424 −1.091 0.001 GO:0001516 prostaglandin biosynthetic process; GO:0001543 ovarian follicle rupture; GO:0002690 positive regulation of leukocyte chemotaxis; GO:0003100 regulation of systemic arterial blood pressure by endothelin; GO:0007204 elevation of cytosolic calcium ion concentration; GO:0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; GO:0008217 regulation of blood pressure; GO:0008284 positive regulation of cell proliferation; GO:0010460 positive regulation of heart rate; GO:0014824 artery smooth muscle Ring finger protein 10 Rnf10 −1.440 −1.069 0.013 GO:0008150 biological process; GO:0045941 positive regulation of transcription Aldolase A, fructose-bisphosphate Aldoa −1.442 1.024 0.016 GO:0001666 response to hypoxia; GO:0006000 fructose metabolic process; GO:0006096 glycolysis; GO:0006754 ATP biosynthetic process; GO:0006941 striated muscle contraction; GO:0008152 metabolic process; GO:0008360 regulation of cell shape; GO:0009408 response to heat; GO:0030388 fructose 1,6-bisphosphate metabolic process; GO:0032496 response to lipopolysaccharide Adenylate cyclase 6 Adcy6 −1.442 −1.031 0.036 GO:0006171 cAMP biosynthetic process; GO:0007193 inhibition of adenylate cyclase activity by G-protein signaling pathway ; GO:0009755 hormone-mediated signaling pathway; GO:0034199 activation of protein kinase A activity UDP-glucose ceramide glucosyltransferase Ugcg −1.443 −1.257 0.001 GO:0006665 sphingolipid metabolic process; GO:0008610 lipid biosynthetic process Nuclear receptor subfamily 3, group C, member 2 Nr3c2 −1.447 −1.092 0.009 GO:0006883 cellular sodium ion homeostasis; GO:0007588 excretion; GO:0031959 mineralocorticoid receptor signaling pathway; GO:0042127 regulation of cell proliferation Inositol polyphosphate-5-phosphatase J Inpp5j −1.455 −1.112 0.023 GO:0010977 negative regulation of neuron projection development; GO:0031115 negative regulation of microtubule polymerization; GO:0033137 negative regulation of peptidyl-serine phosphorylation cytokine-like nuclear factor n-pac N-pac −1.456 −1.106 0.032 GO:0006098 pentose-phosphate shunt; GO:0055114 oxidation reduction Glutamic-oxaloacetic transaminase 2, mitochondrial Got2 −1.458 −1.135 0.017 GO:0006103 2-oxoglutarate metabolic process; GO:0006107 oxaloacetate metabolic process; (aspartate aminotransferase 2) GO:0006520 cellular amino acid metabolic process; GO:0006531 aspartate metabolic process; GO:0006532 aspartate biosynthetic process; GO:0006533 aspartate catabolic process; GO:0006536 glutamate metabolic process; GO:0009058 biosynthetic process; GO:0015908 fatty acid transport; GO:0019550 glutamate catabolic process to aspartate MAX interactor 1 Mxi1 −1.466 −1.047 0.018 GO:0000122 negative regulation of transcription from RNA polymerase II promoter; GO:0006355 regulation of transcription, DNA-dependent Vacuolar protein sorting 52 homolog (S. cerevisiae) Vps52 −1.478 −1.160 0.025 GO:0015031 protein transport Adenosylhomocysteinase Ahcy −1.487 −1.135 0.008 GO:0001666 response to hypoxia; GO:0002439 chronic inflammatory response to antigenic stimulus; GO:0006730 one-carbon metabolic process; GO:0007584 response to nutrient; GO:0008152 metabolic process; GO:0019510 S-adenosylhomocysteine catabolic process; GO:0042745 circadian sleep/wake cycle Meprin 1 alpha Mep1a −1.502 −1.200 0.037 GO:0006508 proteolysis Myosin IE Myo1e −1.516 −1.229 0.004 GO:0001570 vasculogenesis; GO:0001701 in utero embryonic development; GO:0001822 kidney development; GO:0006807 nitrogen compound metabolic process; GO:0030097 hemopoiesis; GO:0035166 post-embiyonic hemopoiesis; GO:0048008 platelet-derived growth factor receptor signaling pathway Lymphocyte antigen 6 complex, locus E Ly6e −1.541 −1.316 0.001 GO:0001701 in utero embryonic development; GO:0030325 adrenal gland development; GO:0035265 organ growth; GO:0042415 norepinephrine metabolic process; GO:0048242 epinephrine secretion; GO:0055010 ventricular cardiac muscle tissue morphogenesis Aldehyde dehydrogenase 1 family, member A1 Aldh1a1 −1.553 1.170 0.023 GO:0001822 kidney development; GO:0001889 liver development; GO:0002072 optic cup morphogenesis involved in camera-type eye development; GO:0006979 response to oxidative stress; GO:0007494 midgut development; GO:0014070 response to organic cyclic substance; GO:0032355 response to estradiol stimulus; GO:0032526 response to retinoic acid; GO:0042493 response to drug; GO:0042572 retinol metabolic process Olfactory receptor 434 Olr434 −1.560 −1.382 0.000 GO:0007186 G-protein coupled receptor protein signaling pathway Olfactory receptor 1607 Olr1607 −1.578 −1.370 0.043 GO:0007186 G-protein coupled receptor protein signaling pathway; GO:0050911 detection of chemical stimulus involved in sensory perception of smell Serine peptidase inhibitor, Kunitz type 1 Spint1 −1.611 −1.093 0.011 GO:0001763 morphogenesis of a branching structure; GO:0001892 embiyonic placenta development; GO:0030198 extracellular matrix organization; GO:0060670 branching involved in embryonic placenta morphogenesis; GO:0060674 placenta blood vessel development D site of albumin promoter (albumin D-box) Dbp −1.647 −1.918 0.000 GO:0006355 regulation of transcription, DNA-dependent; GO:0042127 regulation of cell binding protein proliferation; GO:0048511 rhythmic process Solute carrier family 5 (sodium-dependent vitamin Slc5a6 −1.650 −1.222 0.021 GO:0006811 ion transport; GO:0006814 sodium ion transport; GO:0015878 biotin transport; transporter), member 6 GO:0015887 pantothenate transmembrane transport; GO:0055085 transmembrane transport Multiple inositol polyphosphate histidine Minpp1 −1.658 −1.225 0.010 GO:0048015 phosphoinositide-mediated signaling phosphatase 1 Tsukushin Tsku −1.682 1.012 0.014 Solute carrier family 26, member 3 Slc26a3 −1.724 −1.112 0.034 GO:0006820 anion transport; GO:0008272 sulfate transport; GO:0055085 transmembrane transport Cystathionase (cystathionine gamma-lyase) Cth −1.725 −1.172 0.046 GO:0006520 cellular amino acid metabolic process; GO:0006749 glutathione metabolic process; GO:0008285 negative regulation of cell proliferation; GO:0008652 cellular amino acid biosynthetic process; GO:0018272 protein-pyridoxal-5-phosphate linkage via peptidyl- N6-pyridoxal phosphate-L-lvsine; GO:0019344 cysteine biosynthetic process; GO:0019346 transsulfuration//traceable author statement; GO:0030308 negative regulation of cell growth; GO:0050667 homocysteine metabolic process; GO:0051289 protein homotetramerization Peripheral myelin protein 22 Pmp22 −1.955 −1.443 0.042 GO:0007049 cell cycle; GO:0007050 cell cycle arrest; GO:0008285 negative regulation of cell proliferation; GO:0030154 cell differentiation; GO:0032288 myelin assembly; GO:0042552 myelination Hydroxysteroid 11-beta dehydrogenase 2 Hsd11b2 −2.002 1.001 0.041 GO:0001666 response to hypoxia; GO:0002017 regulation of blood volume by renal aldosterone; GO:0006950 response to stress; GO:0007565 female pregnancy; GO:0008152 metabolic process; GO:0008211 glucocorticoid metabolic process; GO:0032094 response to food; GO:0032868 response to insulin stimulus; GO:0042493 response to drug; GO:0048545 response to steroid hormone stimulus Hydroxysteroid (17-beta) dehydrogenase 2 Hsd17b2 −2.530 −1.603 0.040 GO:0006694 steroid biosynthetic process; GO:0032526 response to retinoic acid; GO:0055114 Nuclear receptor subfamily 1, group D, member 1 | Nr1d1| −2.844 −2.072 0.018 GO:0006355 regulation of transcription, DNA-dependent; GO:0007623 circadian rhythm; thyroid hormone receptor alpha Thra GO:0001502 cartilage condensation; GO:0001503 ossification; GO:0001822 kidney development; GO:0001889 liver development; GO:0002155 regulation of thyroid hormone mediated signaling pathway; GO:0006950 response to stress; GO:0007420 brain development; GO:0007611 learning or memory

REFERENCES

-   Kelly D, Campbell J I, King T P, Grant G, Jansson E A, Coutts A G,     Pettersson S, Conway S. Commensal anaerobic gut bacteria attenuate     inflammation by regulating nuclear-cytoplasmic shuttling of     PPAR-gamma and RelA. Nat Immunol. 2004 January; 5(1):104-12. -   Xu J, Bjursell M K, Himrod J, Deng S, Carmichael L K, Chiang H C,     Hooper L V, Gordon J I. A genomic view of the human-Bacteroides     thetaiotaomicron symbiosis. Science. 2003 Mar. 28; 299(5615):2074-6. -   Wendler W M, Kremmer E, Forster R, Winnacker E L. Identification of     pirin, a novel highly conserved nuclear protein. J Biol Chem. 1997     Mar. 28; 272(13):8482-9. -   Berg, D. J., Davidson, N., Kuhn, R., Muller, W., Menon, S., Holland,     G., Thompson-Snipes, L., Leach, M. W., Rennick, D. Enterocolitis and     colon cancer in interleukin-10-deficient mice are associated with     aberrant cytokine production and CD4+Th1-like responses (1996)     Journal of Clinical Investigation, 98 (4), 1010-1020.

All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in biochemistry and molecular biology or related fields are intended to be within the scope of the following claims. 

1.-71. (canceled)
 72. A method of preventing infection by one or more bacteria or reducing a level of the one or more bacteria in a tissue or an organ in a subject, comprising administering to the subject a pharmaceutical composition that comprises: (i) a pirin-related polypeptide of Bacteroides thetaiotaomicron, wherein the pirin-related polypeptide comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 2, as determined by a sequence alignment performed using a Basic Local Alignment Search Tool algorithm with a gap open penalty of 0, a gap extension penalty of 0, and a Blocks Substitution Matrix of 62; and (ii) a pharmaceutically acceptable excipient, diluent, or carrier.
 73. The method of claim 72, wherein the subject has, or is at risk of developing, loss of gut barrier integrity.
 74. The method of claim 72, wherein the one or more bacteria comprise one or more types of lactose fermenting bacteria, and wherein a level of the one or more types of lactose fermenting bacteria in the tissue or the organ of the subject is reduced.
 75. The method of claim 72, wherein the one or more bacteria comprise one or more types of non-lactose fermenting bacteria, and wherein a level of the one or more types of non-lactose fermenting bacteria in the tissue or the organ of the subject is reduced.
 76. The method of claim 72, wherein the tissue is selected from the group consisting of a mesenteric lymph node, a liver, and a spleen.
 77. The method of claim 72, wherein the administering improves the subject's gut barrier integrity as compared to prior to the administering.
 78. The method of claim 74, wherein the one or more types of lactose fermenting bacteria comprise E. coli, Enterobacter, or Klebsiella.
 79. The method of claim 75, wherein the one or more types of non-lactose fermenting bacteria comprise Salmonella, Proteus, Pseudomonas aeruginosa, or Shigella.
 80. The method of claim 72, wherein the pharmaceutical composition is a solid composition.
 81. The method of claim 72, wherein the pharmaceutical composition is a liquid composition.
 82. The method of claim 72, wherein the pirin-related polypeptide is encapsulated in a capsule.
 83. The method of claim 82, wherein the capsule is an enterically resistant capsule for delivery to an intestine of the subject.
 84. The method of claim 72, wherein the pirin-related polypeptide is Polypeptide Hypothetical Protein (HP).
 85. The method of claim 72, wherein the administering is oral, parenteral, intramuscular, intraperitoneal, subcutaneous, intradermal, or intravenous.
 86. The method of claim 72, wherein the pirin-related polypeptide comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 2, as determined by a sequence alignment performed using a Basic Local Alignment Search Tool algorithm with a gap open penalty of 0, a gap extension penalty of 0, and a Blocks Substitution Matrix of
 62. 87. A method of regulating the expression of one or more pro-inflammatory genes or barrier integrity genes in a cell or cells of a subject, comprising administering to the subject a pharmaceutical composition that comprises: (i) a pirin-related polypeptide of Bacteroides thetaiotaomicron, wherein the pirin-related polypeptide comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 2, as determined by a sequence alignment performed using a Basic Local Alignment Search Tool algorithm with a gap open penalty of 0, a gap extension penalty of 0, and a Blocks Substitution Matrix of 62; and (ii) a pharmaceutically acceptable excipient, diluent, or carrier.
 88. The method of claim 87, wherein the one or more pro-inflammatory genes or barrier integrity genes is selected from the group consisting of regenerating islet-derived 3 beta (Reg3b), resistin-like gamma (Retnlg), resistin-like beta (Retnlb), sucrase-isomaltase (Si), defensin alpha 24 (Defa24), hydroxysteroid 11-beta dehydrogenase 2 (Hsd11b2), hydroxysteroid (17-beta), dehydrogenase 2 (Hsd17b2), resistin-Like Molecule-beta (RELMb), nuclear receptor 1D1 (Nr1d1), and thyroid hormone receptor alpha (Thra).
 89. The method of claim 87, wherein the administering decreases the expression level of a gene selected from the group consisting of Reg3b, Retnlg, Retnlb, Si, and Defa24, relative to the expression level of the gene prior to the administering.
 90. The method of claim 87, wherein the pirin-related polypeptide is Polypeptide Hypothetical Protein (HP).
 91. The method of claim 87, wherein the pirin-related polypeptide comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 2, as determined by a sequence alignment performed using a Basic Local Alignment Search Tool algorithm with a gap open penalty of 0, a gap extension penalty of 0, and a Blocks Substitution Matrix of
 62. 